Gene Ontology Function prediction in Mollicutes using Protein-Protein Association Networks

Abstract Background: Many complex systems can be represented and analysed as networks. The recent availability of large-scale datasets, has made it possible to elucidate some of the organisational principles and rules that govern their function, robustness and evolution. However, one of the main limitations in using protein-protein interactions for function prediction is the availability of interaction data, especially for Mollicutes. If we could harness predicted interactions, such as those from a Protein-Protein Association Networks (PPAN), combining several protein-protein network function-inference methods with semantic similarity calculations, the use of protein-protein interactions for functional inference in this species would become more potentially useful. Results: In this work we show that using PPAN data combined with other approximations, such as functional module detection, orthology exploitation methods and Gene Ontology (GO)-based information measures helps to predict protein function in Mycoplasma genitalium. Conclusions: To our knowledge, the proposed method is the first that combines functional module detection among species, exploiting an orthology procedure and using information theory-based GO semantic similarity in PPAN of the Mycoplasma species. The results of an evaluation show a higher recall than previously reported methods that focused on only one organism network.

Automatic Recognition of Leaves by Shape Detection Pre-Processing with Ica

In this work we present a simulation of a recognition process with perimeter characterization of a simple plant leaves as a unique discriminating parameter. Data coding allowing for independence of leaves size and orientation may penalize performance recognition for some varieties. Border description sequences are then used to characterize the leaves. Independent Component Analysis (ICA) is then applied in order to study which is the best number of components to be considered for the classification task, implemented by means of an Artificial Neural Network (ANN). Obtained results with ICA as a pre-processing tool are satisfactory, and compared with some references our system improves the recognition success up to 80.8% depending on the number of considered independent components.

Symptomatic intracranial hemorrhage after stroke thrombolysis: comparison of prediction scores.

BACKGROUND AND PURPOSE: Several prognostic scores have been developed to predict the risk of symptomatic intracranial hemorrhage (sICH) after ischemic stroke thrombolysis. We compared the performance of these scores in a multicenter cohort. METHODS: We merged prospectively collected data of patients with consecutive ischemic stroke who received intravenous thrombolysis in 7 stroke centers. We identified and evaluated 6 scores that can provide an estimate of the risk of sICH in hyperacute settings: MSS (Multicenter Stroke Survey); HAT (Hemorrhage After Thrombolysis); SEDAN (blood sugar, early infarct signs, [hyper]dense cerebral artery sign, age, NIH Stroke Scale); GRASPS (glucose at presentation, race [Asian], age, sex [male], systolic blood pressure at presentation, and severity of stroke at presentation [NIH Stroke Scale]); SITS (Safe Implementation of Thrombolysis in Stroke); and SPAN (stroke prognostication using age and NIH Stroke Scale)-100 positive index. We included only patients with available variables for all scores. We calculated the area under the receiver operating characteristic curve (AUC-ROC) and also performed logistic regression and the Hosmer-Lemeshow test. RESULTS: The final cohort comprised 3012 eligible patients, of whom 221 (7.3%) had sICH per National Institute of Neurological Disorders and Stroke, 141 (4.7%) per European Cooperative Acute Stroke Study II, and 86 (2.9%) per Safe Implementation of Thrombolysis in Stroke criteria. The performance of the scores assessed with AUC-ROC for predicting European Cooperative Acute Stroke Study II sICH was: MSS, 0.63 (95% confidence interval, 0.58-0.68); HAT, 0.65 (0.60-0.70); SEDAN, 0.70 (0.66-0.73); GRASPS, 0.67 (0.62-0.72); SITS, 0.64 (0.59-0.69); and SPAN-100 positive index, 0.56 (0.50-0.61). SEDAN had significantly higher AUC-ROC values compared with all other scores, except for GRASPS where the difference was nonsignificant. SPAN-100 performed significantly worse compared with other scores. The discriminative ranking of the scores was the same for the National Institute of Neurological Disorders and Stroke, and Safe Implementation of Thrombolysis in Stroke definitions, with SEDAN performing best, GRASPS second, and SPAN-100 worst. CONCLUSIONS: SPAN-100 had the worst predictive power, and SEDAN constantly the highest predictive power. However, none of the scores had better than moderate performance.

Prediction of Childhood Asthma Using Conditional Probability and Discrete Event Simulation

Abstract: Asthma prevalence in children and adolescents in Spain is 10-17%. It is the most common chronic illness during childhood. Prevalence has been increasing over the last 40 years and there is considerable evidence that, among other factors, continued exposure to cigarette smoke results in asthma in children. No statistical or simulation model exist to forecast the evolution of childhood asthma in Europe. Such a model needs to incorporate the main risk factors that can be managed by medical authorities, such as tobacco (OR = 1.44), to establish how they affect the present generation of children. A simulation model using conditional probability and discrete event simulation for childhood asthma was developed and validated by simulating realistic scenario. The parameters used for the model (input data) were those found in the bibliography, especially those related to the incidence of smoking in Spain. We also used data from a panel of experts from the Hospital del Mar (Barcelona) related to actual evolution and asthma phenotypes. The results obtained from the simulation established a threshold of a 15-20% smoking population for a reduction in the prevalence of asthma. This is still far from the current level in Spain, where 24% of people smoke. We conclude that more effort must be made to combat smoking and other childhood asthma risk factors, in order to significantly reduce the number of cases. Once completed, this simulation methodology can realistically be used to forecast the evolution of childhood asthma as a function of variation in different risk factors.

Investigation of Rapid Thermal Analysis Procedures for Prediction of the Service Life of PCCP Carbonate Coarse Aggregate, HR-337, 1993

The major objective of this research project was to use thermal analysis techniques in conjunction with x-ray analysis methods to identify and explain chemical reactions that promote aggregate related deterioration in portland cement concrete. Twenty-two different carbonate aggregate samples were subjected to a chemical testing scheme that included: • bulk chemistry (major, minor and selected trace elements) • bulk mineralogy (minor phases concentrated by acid extraction) • solid-solution in the major carbonate phases • crystallite size determinations for the major carbonate phases • a salt treatment study to evaluate the impact of deicer salts Test results from these different studies were then compared to information that had been obtained using thermogravimetric analysis techniques. Since many of the limestones and dolomites that were used in the study had extensive field service records it was possible to correlate many of the variables with service life. The results of this study have indicated that thermogravimetric analysis can play an important role in categorizing carbonate aggregates. In fact, with modern automated thermal analysis systems it should be possible to utilize such methods on a quality control basis. Strong correlations were found between several of the variables that were monitored in this study. In fact, several of the variables exhibited significant correlations to concrete service life. When the full data set was utilized (n = 18), the significant correlations to service life can be summarized as follows ( a = 5% level): • Correlation coefficient, r, = -0.73 for premature TG loss versus service life. • Correlation coefficient, r, = 0.74 for relative crystallite size versus service life. • Correlation coefficient, r, = 0.53 for ASTM C666 durability factor versus service life. • Correlation coefficient, r, = -0.52 for acid-insoluble residue versus service life. Separation of the carbonate aggregates into their mineralogical categories (i.e., calcites and dolomites) tended to increase the correlation coefficients for some specific variables (r sometimes approached 0.90); however, the reliability of such correlations was questionable because of the small number of samples that were present in this study.

Prediction of cottonseed longevity

The objective of this work was to determine the viability equation constants for cottonseed and to detect the occurrence and depletion of hardseededness. Three seedlots of Brazilian cultivars IAC-19 and IAC-20 were tested, using 12 moisture content levels, ranging from 2.2 to 21.7% and three storage temperatures, 40, 50 and 65ºC. Seed moisture content level was reached from the initial value (around 8.8%) either by rehydration, in a closed container, or by drying in desiccators containing silica gel, both at 20ºC. Twelve seed subsamples for each moisture content/temperature treatment were sealed in laminated aluminium-foil packets and stored in incubators at those temperatures, until complete survival curves were obtained. Seed equilibrium relative humidity was recorded. Hardseededness was detected at moisture content levels below 6% and its releasing was achieved either naturally, during storage period, or artificially through seed coat removal. The viability equation quantified the response of seed longevity to storage environment well with K E = 9.240, C W = 5.190, C H = 0.03965 and C Q = 0.000426. The lower limit estimated for application of this equation at 65ºC was 3.6% moisture content.

Ferromagnetic shape memory alloys: structural and thermal properties

The most extensively studied Heusler alloys are those based on the Ni-Mn-Ga system. However, to overcome the high cost of Gallium and the usually low martensitic transformation temperature, the search for Ga-free alloys has been recently attempted, particularly, by introducing In, Sn or Sb. In this work, two alloys (Mn50Ni35.5In14.5 and Ni50Mn35In15) have been obtained by melt spinning. We outline their structural and thermal behaviour. Mn50Ni35.5In14.5 alloy has the transformation above room temperature whereas Ni50Mn35In15 does not have this transformation in the temperature range here analyzed

Improvement of walking speed prediction by accelerometry and altimetry, validated by satellite positioning.

Activity monitors based on accelerometry are used to predict the speed and energy cost of walking at 0% slope, but not at other inclinations. Parallel measurements of body accelerations and altitude variation were studied to determine whether walking speed prediction could be improved. Fourteen subjects walked twice along a 1.3 km circuit with substantial slope variations (-17% to +17%). The parameters recorded were body acceleration using a uni-axial accelerometer, altitude variation using differential barometry, and walking speed using satellite positioning (DGPS). Linear regressions were calculated between acceleration and walking speed, and between acceleration/altitude and walking speed. These predictive models, calculated using the data from the first circuit run, were used to predict speed during the second circuit. Finally the predicted velocity was compared with the measured one. The result was that acceleration alone failed to predict speed (mean r = 0.4). Adding altitude variation improved the prediction (mean r = 0.7). With regard to the altitude/acceleration-speed relationship, substantial inter-individual variation was found. It is concluded that accelerometry, combined with altitude measurement, can assess position variations of humans provided inter-individual variation is taken into account. It is also confirmed that DGPS can be used for outdoor walking speed measurements, opening up new perspectives in the field of biomechanics.

Scour Around Bridge Piers and Abutments, HR-30 and Iowa Highway Research Board Bulletin No. 4, 1956

Man’s never-ending search for better materials and construction methods and for techniques of analysis and design has overcome most of the early difficulties of bridge building. Scour of the stream bed, however, has remained a major cause of bridge failures ever since man learned to place piers and abutments in the stream in order to cross wide rivers. Considering the overall complexity of field conditions, it is not surprising that no generally accepted principles (not even rules of thumb) for the prediction of scour around bridge piers and abutments have evolved from field experience alone. The flow of individual streams exhibits a manifold variation, and great disparity exists among different rivers. The alignment, cross section, discharge, and slope of a stream must all be correlated with the scour phenomenon, and this in turn must be correlated with the characteristics of the bed material ranging from clays and fine silts to gravels and boulders. Finally, the effect of the shape of the obstruction itself-the pier or abutment-must be assessed. Since several of these factors are likely to vary with time to some degree, and since the scour phenomenon as well is inherently unsteady, sorting out the influence of each of the various factors is virtually impossible from field evidence alone. The experimental approach was chosen as the investigative method for this study, but with due recognition of the importance of field measurements and with the realization that the results must be interpreted so as to be compatible with the present-day theories of fluid mechanics and sediment transportation. This approach was chosen because, on the one hand, the factors affecting the scour phenomenon can be controlled in the laboratory to an extent that is not possible in the field, and, on the other hand, the model technique can be used to circumvent the present inadequate understanding of the phenomenon of the movement of sediment by flowing water. In order to obtain optimum results from the laboratory study, the program was arranged at the outset to include a related set of variables in each of several phases into which the whole problem was divided. The phases thus selected were : 1. Geometry of piers and abutments, 2. Hydraulics of the stream, 3. Characteristics of the sediment, 4. Geometry of channel shape and alignment.

Fluid dynamical prediction of changed v1-flow at energies available at the CERN Large Hadron Collider

Substantial collective flow is observed in collisions between lead nuclei at Large Hadron Collider (LHC) as evidenced by the azimuthal correlations in the transverse momentum distributions of the produced particles. Our calculations indicate that the global v1-flow, which at RHIC peaked at negative rapidities (named third flow component or antiflow), now at LHC is going to turn toward forward rapidities (to the same side and direction as the projectile residue). Potentially this can provide a sensitive barometer to estimate the pressure and transport properties of the quark-gluon plasma. Our calculations also take into account the initial state center-of-mass rapidity fluctuations, and demonstrate that these are crucial for v1 simulations. In order to better study the transverse momentum flow dependence we suggest a new"symmetrized" vS1(pt) function, and we also propose a new method to disentangle global v1 flow from the contribution generated by the random fluctuations in the initial state. This will enhance the possibilities of studying the collective Global v1 flow both at the STAR Beam Energy Scan program and at LHC.

V3 net charge: additional tool in HIV-1 tropism prediction.

Genotype-based algorithms are valuable tools for the identification of patients eligible for CCR5 inhibitors administration in clinical practice. Among the available methods, geno2pheno[coreceptor] (G2P) is the most used online tool for tropism prediction. This study was conceived to assess if the combination of G2P prediction with V3 peptide net charge (NC) value could improve the accuracy of tropism prediction. A total of 172 V3 bulk sequences from 143 patients were analyzed by G2P and NC values. A phenotypic assay was performed by cloning the complete env gene and tropism determination was assessed on U87_CCR5(+)/CXCR4(+) cells. Sequences were stratified according to the agreement between NC values and G2P results. Of sequences predicted as X4 by G2P, 61% showed NC values higher than 5; similarly, 76% of sequences predicted as R5 by G2P had NC values below 4. Sequences with NC values between 4 and 5 were associated with different G2P predictions: 65% of samples were predicted as R5-tropic and 35% of sequences as X4-tropic. Sequences identified as X4 by NC value had at least one positive residue at positions known to be involved in tropism prediction and positive residues in position 32. These data supported the hypothesis that NC values between 4 and 5 could be associated with the presence of dual/mixed-tropic (DM) variants. The phenotypic assay performed on a subset of sequences confirmed the tropism prediction for concordant sequences and showed that NC values between 4 and 5 are associated with DM tropism. These results suggest that the combination of G2P and NC could increase the accuracy of tropism prediction. A more reliable identification of X4 variants would be useful for better selecting candidates for Maraviroc (MVC) administration, but also as a predictive marker in coreceptor switching, strongly associated with the phase of infection.