Intrinsically Multivariate Predictive Genes

Canalizing genes possess such broad regulatory power, and their action sweeps across a such a wide swath of processes that the full set of affected genes are not highly correlated under normal conditions. When not active, the controlling gene will not be predictable to any significant degree by its subject genes, either alone or in groups, since their behavior will be highly varied relative to the inactive controlling gene. When the controlling gene is active, its behavior is not well predicted by any one of its targets, but can be very well predicted by groups of genes under its control. To investigate this question, we introduce in this paper the concept of intrinsically multivariate predictive (IMP) genes, and present a mathematical study of IMP in the context of binary genes with respect to the coefficient of determination (CoD), which measures the predictive power of a set of genes with respect to a target gene. A set of predictor genes is said to be IMP for a target gene if all properly contained subsets of the predictor set are bad predictors of the target but the full predictor set predicts the target with great accuracy. We show that logic of prediction, predictive power, covariance between predictors, and the entropy of the joint probability distribution of the predictors jointly affect the appearance of IMP genes. In particular, we show that high-predictive power, small covariance among predictors, a large entropy of the joint probability distribution of predictors, and certain logics, such as XOR in the 2-predictor case, are factors that favor the appearance of IMP. The IMP concept is applied to characterize the behavior of the gene DUSP1, which exhibits control over a central, process-integrating signaling pathway, thereby providing preliminary evidence that IMP can be used as a criterion for discovery of canalizing genes.

Signal propagation in Bayesian networks and its relationship with intrinsically multivariate predictive variables

A set of predictor variables is said to be intrinsically multivariate predictive (IMP) for a target variable if all properly contained subsets of the predictor set are poor predictors of the. target but the full set predicts the target with great accuracy. In a previous article, the main properties of IMP Boolean variables have been analytically described, including the introduction of the IMP score, a metric based on the coefficient of determination (CoD) as a measure of predictiveness with respect to the target variable. It was shown that the IMP score depends on four main properties: logic of connection, predictive power, covariance between predictors and marginal predictor probabilities (biases). This paper extends that work to a broader context, in an attempt to characterize properties of discrete Bayesian networks that contribute to the presence of variables (network nodes) with high IMP scores. We have found that there is a relationship between the IMP score of a node and its territory size, i.e., its position along a pathway with one source: nodes far from the source display larger IMP scores than those closer to the source, and longer pathways display larger maximum IMP scores. This appears to be a consequence of the fact that nodes with small territory have larger probability of having highly covariate predictors, which leads to smaller IMP scores. In addition, a larger number of XOR and NXOR predictive logic relationships has positive influence over the maximum IMP score found in the pathway. This work presents analytical results based on a simple structure network and an analysis involving random networks constructed by computational simulations. Finally, results from a real Bayesian network application are provided. (C) 2012 Elsevier Inc. All rights reserved.

Multivariate prediction

The problem of prediction is considered in a multidimensional setting. Extending an idea presented by Barndorff-Nielsen and Cox, a predictive density for a multivariate random variable of interest is proposed. This density has the form of an estimative density plus a correction term. It gives simultaneous prediction regions with coverage error of smaller asymptotic order than the estimative density. A simulation study is also presented showing the magnitude of the improvement with respect to the estimative method.

Application of the Multivariate Prediction Method to Time Series

* This work was financially supported by RFBR-04-01-00858.

Factores asociados a complicaciones post quirúrgicas en pacientes adultos con obstrucción intestinal mecánica en Bogotá, Colombia, período 2008 - 2014

Introducción: La obstrucción intestinal es una patología de alta prevalencia e impacto en los servicios de cirugía general a nivel mundial. El manejo de esta entidad puede ser médico o quirúrgico. Cuando se requiere intervención quirúrgica, se busca evitar el desarrollo de isquemia intestinal y resecciones intestinales; durante el postoperatorio, pueden existir complicaciones. El objetivo de este estudio es identificar los factores asociados al desarrollo de complicaciones post operatorias en un grupo de pacientes con obstrucción intestinal mecánica llevados a manejo quirúrgico. Metodología: Estudio analítico tipo casos y controles en un grupo de pacientes con diagnóstico de obstrucción intestinal mecánica llevados a manejo quirúrgico de su patología. Los casos corresponden a los pacientes con complicaciones postoperatorias y los controles aquellos que no presentaron complicaciones. Se identificaron factores asociados a complicación post operatoria mediante modelos estadísticos bivariados y multivariados de regresión logística para factores como edad, sexo, antecedente quirúrgico, presentación clínica, paraclínica y diagnóstico postoperatorio de malignidad, entre otras. Resultados: Se identificaron un total de 138 pacientes (54 casos y 129 controles). Los rangos de edad entre 55-66 años y mayor de 66 años fueron asociados con complicaciones postoperatorias (OR 3,87 IC95% 1,58-9,50 y OR 3,62 IC95% 1,45-9,08 respectivamente). El déficit de base inferior a 5 mEq/litro se relaciona con complicaciones postoperatorias (OR 2,64 IC95% 1.33-5,25) Otras pruebas de laboratorio, características radiológicas, hallazgos de malignidad en el postoperatorio y la evolución de los pacientes no fueron asociados con complicaciones. Conclusiones: Las disminución de las complicaciones durante el manejo quirúrgico de obstrucción intestinal mecánica continúa siendo un reto para la cirugía general. Factores no modificables como edad avanzada y modificables como el equilibrio ácido base deben ser tenidos en cuenta dada su correlación en el desarrollo de complicaciones postoperatorias.

Factores asociados a tratamiento quirúrgico en pacientes con obstrucción intestinal por adherencias

El manejo de la obstrucción intestinal por adherencias es un reto para cualquier especialista en Cirugía debido a que existe controversia sobre el alcance del manejo médico y el momento adecuado para llevar el paciente a cirugía para la resolución del cuadro clínico. En el presente trabajo se pretende, identificar los factores asociados a tratamiento quirúrgico en pacientes con obstrucción intestinal por adherencias. Metodología: Se realizó un estudio de casos y controles en una relación de 1:1, con una recolección de muestra estadística de 48 pacientes en cada grupo, entre mayo 2012 y mayo 2014 en el Hospital Universitario Mayor Mederi y en Barrios Unidos. Se consideraron casos los pacientes intervenidos quirúrgicamente por obstrucción intestinal por bridas y controles los pacientes manejados con tratamiento médico. Se evaluaron factores como edad, antecedentes personales patológicos y quirúrgicos, tiempo de evolución del cuadro clínico, hallazgos en imágenes y laboratorio entre otros. Resultados: Se recolectaron un total de 158 pacientes, (78 casos, 80 controles). Ambas poblaciones fueron comparables (p=0.13). Los factores asociados a tratamiento quirúrgico estadísticamente significativos fueron género masculino, presencia de fiebre al ingreso, el hallazgo de engrosamiento de la pared intestinal y de obstrucción de asa cerrada en imágenes diagnósticas (p<0,05). Discusión: Los principales factores asociados para que un paciente con obstrucción intestinal por bridas requiera de manejo quirúrgico son consistentes con literatura. Se requiere la socialización de los resultados para disminuir la morbimortalidad de nuestros pacientes.

Carbon Nuclear Magnetic Resonance Spectroscopic Profiles coupled to Partial Least-Squares Multivariate Regression for Prediction of Several Physicochemical Parameters of Brazilian Commercial Gasoline

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Multivariate calibrations on H-1 NMR profiles for prediction of physicochemical parameters of Brazilian commercial gasoline

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Multivariate calibrations in gas chromatographic profiles for prediction of several physicochemical parameters of Brazilian commercial gasoline

Several Brazilian commercial gasoline physicochemical parameters, such as relative density, distillation curve (temperatures related to 10%, 50% and 90% of distilled volume, final boiling point and residue), octane numbers (motor and research octane number and anti-knock index), hydrocarbon compositions (olefins, aromatics and saturates) and anhydrous ethanol and benzene content was predicted from chromatographic profiles obtained by flame ionization detection (GC-FID) and using partial least square regression (PLS). GC-FID is a technique intensively used for fuel quality control due to its convenience, speed, accuracy and simplicity and its profiles are much easier to interpret and understand than results produced by other techniques. Another advantage is that it permits association with multivariate methods of analysis, such as PLS. The chromatogram profiles were recorded and used to deploy PLS models for each property. The standard error of prediction (SEP) has been the main parameter considered to select the "best model". Most of GC-FID-PLS results, when compared to those obtained by the Brazilian Government Petroleum, Natural Gas and Biofuels Agency - ANP Regulation 309 specification methods, were very good. In general, all PLS models developed in these work provide unbiased predictions with lows standard error of prediction and percentage average relative error (below 11.5 and 5.0, respectively). (C) 2007 Elsevier B.V. All rights reserved.

Toward prediction of class II mouse major histocompatibility complex peptide binding affinity:in silico bioinformatic evaluation using partial least squares, a robust multivariate statistical technique

The accurate identification of T-cell epitopes remains a principal goal of bioinformatics within immunology. As the immunogenicity of peptide epitopes is dependent on their binding to major histocompatibility complex (MHC) molecules, the prediction of binding affinity is a prerequisite to the reliable prediction of epitopes. The iterative self-consistent (ISC) partial-least-squares (PLS)-based additive method is a recently developed bioinformatic approach for predicting class II peptide−MHC binding affinity. The ISC−PLS method overcomes many of the conceptual difficulties inherent in the prediction of class II peptide−MHC affinity, such as the binding of a mixed population of peptide lengths due to the open-ended class II binding site. The method has applications in both the accurate prediction of class II epitopes and the manipulation of affinity for heteroclitic and competitor peptides. The method is applied here to six class II mouse alleles (I-Ab, I-Ad, I-Ak, I-As, I-Ed, and I-Ek) and included peptides up to 25 amino acids in length. A series of regression equations highlighting the quantitative contributions of individual amino acids at each peptide position was established. The initial model for each allele exhibited only moderate predictivity. Once the set of selected peptide subsequences had converged, the final models exhibited a satisfactory predictive power. Convergence was reached between the 4th and 17th iterations, and the leave-one-out cross-validation statistical terms - q2, SEP, and NC - ranged between 0.732 and 0.925, 0.418 and 0.816, and 1 and 6, respectively. The non-cross-validated statistical terms r2 and SEE ranged between 0.98 and 0.995 and 0.089 and 0.180, respectively. The peptides used in this study are available from the AntiJen database (http://www.jenner.ac.uk/AntiJen). The PLS method is available commercially in the SYBYL molecular modeling software package. The resulting models, which can be used for accurate T-cell epitope prediction, will be made freely available online (http://www.jenner.ac.uk/MHCPred).

Using multivariate sequential patterns to improve survival prediction in intensive care burn unit

Resuscitation and stabilization are key issues in Intensive Care Burn Units and early survival predictions help to decide the best clinical action during these phases. Current survival scores of burns focus on clinical variables such as age or the body surface area. However, the evolution of other parameters (e.g. diuresis or fluid balance) during the first days is also valuable knowledge. In this work we suggest a methodology and we propose a Temporal Data Mining algorithm to estimate the survival condition from the patient’s evolution. Experiments conducted on 480 patients show the improvement of survival prediction.

Comparing Near-infrared Conventional Diffuse Reflectance Spectroscopy And Hyperspectral Imaging For Determination Of The Bulk Properties Of Solid Samples By Multivariate Regression: Determination Of Mooney Viscosity And Plasticity Indices Of Natural Rubber.

Conventional reflectance spectroscopy (NIRS) and hyperspectral imaging (HI) in the near-infrared region (1000-2500 nm) are evaluated and compared, using, as the case study, the determination of relevant properties related to the quality of natural rubber. Mooney viscosity (MV) and plasticity indices (PI) (PI0 - original plasticity, PI30 - plasticity after accelerated aging, and PRI - the plasticity retention index after accelerated aging) of rubber were determined using multivariate regression models. Two hundred and eighty six samples of rubber were measured using conventional and hyperspectral near-infrared imaging reflectance instruments in the range of 1000-2500 nm. The sample set was split into regression (n = 191) and external validation (n = 95) sub-sets. Three instruments were employed for data acquisition: a line scanning hyperspectral camera and two conventional FT-NIR spectrometers. Sample heterogeneity was evaluated using hyperspectral images obtained with a resolution of 150 × 150 μm and principal component analysis. The probed sample area (5 cm(2); 24,000 pixels) to achieve representativeness was found to be equivalent to the average of 6 spectra for a 1 cm diameter probing circular window of one FT-NIR instrument. The other spectrophotometer can probe the whole sample in only one measurement. The results show that the rubber properties can be determined with very similar accuracy and precision by Partial Least Square (PLS) regression models regardless of whether HI-NIR or conventional FT-NIR produce the spectral datasets. The best Root Mean Square Errors of Prediction (RMSEPs) of external validation for MV, PI0, PI30, and PRI were 4.3, 1.8, 3.4, and 5.3%, respectively. Though the quantitative results provided by the three instruments can be considered equivalent, the hyperspectral imaging instrument presents a number of advantages, being about 6 times faster than conventional bulk spectrometers, producing robust spectral data by ensuring sample representativeness, and minimizing the effect of the presence of contaminants.

Keratoconus prediction using a finite element model of the cornea with local biomechanical properties

PURPOSE: The ability to predict and understand which biomechanical properties of the cornea are responsible for the stability or progression of keratoconus may be an important clinical and surgical tool for the eye-care professional. We have developed a finite element model of the cornea, that tries to predicts keratoconus-like behavior and its evolution based on material properties of the corneal tissue. METHODS: Corneal material properties were modeled using bibliographic data and corneal topography was based on literature values from a schematic eye model. Commercial software was used to simulate mechanical and surface properties when the cornea was subject to different local parameters, such as elasticity. RESULTS: The simulation has shown that, depending on the corneal initial surface shape, changes in local material properties and also different intraocular pressures values induce a localized protuberance and increase in curvature when compared to the remaining portion of the cornea. CONCLUSIONS: This technique provides a quantitative and accurate approach to the problem of understanding the biomechanical nature of keratoconus. The implemented model has shown that changes in local material properties of the cornea and intraocular pressure are intrinsically related to keratoconus pathology and its shape/curvature.

Estimation of hexenuronic acids and kappa number in kraft pulps of Eucalyptus globulus by Fourier transform near infrared spectroscopy and multivariate analysis

Fourier transform near infrared (FT-NIR) spectroscopy was evaluated as an analytical too[ for monitoring residual Lignin, kappa number and hexenuronic acids (HexA) content in kraft pulps of Eucalyptus globulus. Sets of pulp samples were prepared under different cooking conditions to obtain a wide range of compound concentrations that were characterised by conventional wet chemistry analytical methods. The sample group was also analysed using FT-NIR spectroscopy in order to establish prediction models for the pulp characteristics. Several models were applied to correlate chemical composition in samples with the NIR spectral data by means of PCR or PLS algorithms. Calibration curves were built by using all the spectral data or selected regions. Best calibration models for the quantification of lignin, kappa and HexA were proposed presenting R-2 values of 0.99. Calibration models were used to predict pulp titers of 20 external samples in a validation set. The lignin concentration and kappa number in the range of 1.4-18% and 8-62, respectively, were predicted fairly accurately (standard error of prediction, SEP 1.1% for lignin and 2.9 for kappa). The HexA concentration (range of 5-71 mmol kg(-1) pulp) was more difficult to predict and the SEP was 7.0 mmol kg(-1) pulp in a model of HexA quantified by an ultraviolet (UV) technique and 6.1 mmol kg(-1) pulp in a model of HexA quantified by anion-exchange chromatography (AEC). Even in wet chemical procedures used for HexA determination, there is no good agreement between methods as demonstrated by the UV and AEC methods described in the present work. NIR spectroscopy did provide a rapid estimate of HexA content in kraft pulps prepared in routine cooking experiments.

ANNA: A new prediction method for bioassessment programs

1. Cluster analysis of reference sites with similar biota is the initial step in creating River Invertebrate Prediction and Classification System (RIVPACS) and similar river bioassessment models such as Australian River Assessment System (AUSRIVAS). This paper describes and tests an alternative prediction method, Assessment by Nearest Neighbour Analysis (ANNA), based on the same philosophy as RIVPACS and AUSRIVAS but without the grouping step that some people view as artificial. 2. The steps in creating ANNA models are: (i) weighting the predictor variables using a multivariate approach analogous to principal axis correlations, (ii) calculating the weighted Euclidian distance from a test site to the reference sites based on the environmental predictors, (iii) predicting the faunal composition based on the nearest reference sites and (iv) calculating an observed/expected (O/E) analogous to RIVPACS/AUSRIVAS. 3. The paper compares AUSRIVAS and ANNA models on 17 datasets representing a variety of habitats and seasons. First, it examines each model's regressions for Observed versus Expected number of taxa, including the r(2), intercept and slope. Second, the two models' assessments of 79 test sites in New Zealand are compared. Third, the models are compared on test and presumed reference sites along a known trace metal gradient. Fourth, ANNA models are evaluated for western Australia, a geographically distinct region of Australia. The comparisons demonstrate that ANNA and AUSRIVAS are generally equivalent in performance, although ANNA turns out to be potentially more robust for the O versus E regressions and is potentially more accurate on the trace metal gradient sites. 4. The ANNA method is recommended for use in bioassessment of rivers, at least for corroborating the results of the well established AUSRIVAS- and RIVPACS-type models, if not to replace them.