Evaluation of peak-picking algorithms for protein mass spectrometry

Peak picking is an early key step in MS data analysis. We compare three commonly used approaches to peak picking and discuss their merits by means of statistical analysis. Methods investigated encompass signal-to-noise ratio, continuous wavelet transform, and a correlation-based approach using a Gaussian template. Functionality of the three methods is illustrated and discussed in a practical context using a mass spectral data set created with MALDI-TOF technology. Sensitivity and specificity are investigated using a manually defined reference set of peaks. As an additional criterion, the robustness of the three methods is assessed by a perturbation analysis and illustrated using ROC curves.

The evaluation of CloudSat and CALIPSO ice microphysical products using ground-based cloud radar and lidar observations

In this paper, the statistical properties of tropical ice clouds (ice water content, visible extinction, effective radius, and total number concentration) derived from 3 yr of ground-based radar–lidar retrievals from the U.S. Department of Energy Atmospheric Radiation Measurement Climate Research Facility in Darwin, Australia, are compared with the same properties derived using the official CloudSat microphysical retrieval methods and from a simpler statistical method using radar reflectivity and air temperature. It is shown that the two official CloudSat microphysical products (2B-CWC-RO and 2B-CWC-RVOD) are statistically virtually identical. The comparison with the ground-based radar–lidar retrievals shows that all satellite methods produce ice water contents and extinctions in a much narrower range than the ground-based method and overestimate the mean vertical profiles of microphysical parameters below 10-km height by over a factor of 2. Better agreements are obtained above 10-km height. Ways to improve these estimates are suggested in this study. Effective radii retrievals from the standard CloudSat algorithms are characterized by a large positive bias of 8–12 μm. A sensitivity test shows that in response to such a bias the cloud longwave forcing is increased from 44.6 to 46.9 W m−2 (implying an error of about 5%), whereas the negative cloud shortwave forcing is increased from −81.6 to −82.8 W m−2. Further analysis reveals that these modest effects (although not insignificant) can be much larger for optically thick clouds. The statistical method using CloudSat reflectivities and air temperature was found to produce inaccurate mean vertical profiles and probability distribution functions of effective radius. This study also shows that the retrieval of the total number concentration needs to be improved in the official CloudSat microphysical methods prior to a quantitative use for the characterization of tropical ice clouds. Finally, the statistical relationship used to produce ice water content from extinction and air temperature obtained by the Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) satellite is evaluated for tropical ice clouds. It is suggested that the CALIPSO ice water content retrieval is robust for tropical ice clouds, but that the temperature dependence of the statistical relationship used should be slightly refined to better reproduce the radar–lidar retrievals.

The statistical properties of tropical ice clouds generated by the West-African and Australian monsoons from ground-based radar-lidar observations

In the present paper we characterize the statistical properties of non-precipitating tropical ice clouds (deep ice anvils resulting from deep convection and cirrus clouds) over Niamey, Niger, West Africa, and Darwin, northern Australia, using ground-based radar–lidar observations from the Atmospheric Radiation Measurement (ARM) programme. The ice cloud properties analysed in this paper are the frequency of ice cloud occurrence, cloud fraction, the morphological properties (cloud-top height, base height, and thickness), the microphysical and radiative properties (ice water content, visible extinction, effective radius, terminal fall speed, and concentration), and the internal cloud dynamics (in-cloud vertical air velocity). The main highlight of the paper is that it characterizes for the first time the probability density functions of the tropical ice cloud properties, their vertical variability and their diurnal variability at the same time. This is particularly important over West Africa, since the ARM deployment in Niamey provides the first vertically resolved observations of non-precipitating ice clouds in this crucial area in terms of redistribution of water and energy in the troposphere. The comparison between the two sites also provides an additional observational basis for the evaluation of the parametrization of clouds in large-scale models, which should be able to reproduce both the statistical properties at each site and the differences between the two sites. The frequency of ice cloud occurrence is found to be much larger over Darwin when compared to Niamey, and with a much larger diurnal variability, which is well correlated with the diurnal cycle of deep convective activity. The diurnal cycle of the ice cloud occurrence over Niamey is also much less correlated with that of deep convective activity than over Darwin, probably owing to the fact that Niamey is further away from the deep convective sources of the region. The frequency distributions of cloud fraction are strongly bimodal and broadly similar over the two sites, with a predominance of clouds characterized either by a very small cloud fraction (less than 0.3) or a very large cloud fraction (larger than 0.9). The ice clouds over Darwin are also much thicker (by 1 km or more statistically) and are characterized by a much larger diurnal variability than ice clouds over Niamey. Ice clouds over Niamey are also characterized by smaller particle sizes and fall speeds but in much larger concentrations, thereby carrying more ice water and producing more visible extinction than the ice clouds over Darwin. It is also found that there is a much larger occurrence of downward in-cloud air motions less than 1 m s−1 over Darwin, which together with the larger fall speeds retrieved over Darwin indicates that the life cycle of ice clouds is probably shorter over Darwin than over Niamey.

Evaluation of ice cloud representation in the ECMWF and UK Met Office models using CloudSat and CALIPSO data

Ice cloud representation in general circulation models remains a challenging task, due to the lack of accurate observations and the complexity of microphysical processes. In this article, we evaluate the ice water content (IWC) and ice cloud fraction statistical distributions from the numerical weather prediction models of the European Centre for Medium-Range Weather Forecasts (ECMWF) and the UK Met Office, exploiting the synergy between the CloudSat radar and CALIPSO lidar. Using the last three weeks of July 2006, we analyse the global ice cloud occurrence as a function of temperature and latitude and show that the models capture the main geographical and temperature-dependent distributions, but overestimate the ice cloud occurrence in the Tropics in the temperature range from −60 °C to −20 °C and in the Antarctic for temperatures higher than −20 °C, but underestimate ice cloud occurrence at very low temperatures. A global statistical comparison of the occurrence of grid-box mean IWC at different temperatures shows that both the mean and range of IWC increases with increasing temperature. Globally, the models capture most of the IWC variability in the temperature range between −60 °C and −5 °C, and also reproduce the observed latitudinal dependencies in the IWC distribution due to different meteorological regimes. Two versions of the ECMWF model are assessed. The recent operational version with a diagnostic representation of precipitating snow and mixed-phase ice cloud fails to represent the IWC distribution in the −20 °C to 0 °C range, but a new version with prognostic variables for liquid water, ice and snow is much closer to the observed distribution. The comparison of models and observations provides a much-needed analysis of the vertical distribution of IWC across the globe, highlighting the ability of the models to reproduce much of the observed variability as well as the deficiencies where further improvements are required.

Downscaling from GCM precipitation: a benchmark for dynamical and statistical downscaling methods

A precipitation downscaling method is presented using precipitation from a general circulation model (GCM) as predictor. The method extends a previous method from monthly to daily temporal resolution. The simplest form of the method corrects for biases in wet-day frequency and intensity. A more sophisticated variant also takes account of flow-dependent biases in the GCM. The method is flexible and simple to implement. It is proposed here as a correction of GCM output for applications where sophisticated methods are not available, or as a benchmark for the evaluation of other downscaling methods. Applied to output from reanalyses (ECMWF, NCEP) in the region of the European Alps, the method is capable of reducing large biases in the precipitation frequency distribution, even for high quantiles. The two variants exhibit similar performances, but the ideal choice of method can depend on the GCM/reanalysis and it is recommended to test the methods in each case. Limitations of the method are found in small areas with unresolved topographic detail that influence higher-order statistics (e.g. high quantiles). When used as benchmark for three regional climate models (RCMs), the corrected reanalysis and the RCMs perform similarly in many regions, but the added value of the latter is evident for high quantiles in some small regions.

Aerosol indirect effects – general circulation model intercomparison and evaluation with satellite data

Aerosol indirect effects continue to constitute one of the most important uncertainties for anthropogenic climate perturbations. Within the international AEROCOM initiative, the representation of aerosol-cloud-radiation interactions in ten different general circulation models (GCMs) is evaluated using three satellite datasets. The focus is on stratiform liquid water clouds since most GCMs do not include ice nucleation effects, and none of the model explicitly parameterises aerosol effects on convective clouds. We compute statistical relationships between aerosol optical depth (τa) and various cloud and radiation quantities in a manner that is consistent between the models and the satellite data. It is found that the model-simulated influence of aerosols on cloud droplet number concentration (Nd ) compares relatively well to the satellite data at least over the ocean. The relationship between �a and liquid water path is simulated much too strongly by the models. This suggests that the implementation of the second aerosol indirect effect mainly in terms of an autoconversion parameterisation has to be revisited in the GCMs. A positive relationship between total cloud fraction (fcld) and �a as found in the satellite data is simulated by the majority of the models, albeit less strongly than that in the satellite data in most of them. In a discussion of the hypotheses proposed in the literature to explain the satellite-derived strong fcld–�a relationship, our results indicate that none can be identified as a unique explanation. Relationships similar to the ones found in satellite data between �a and cloud top temperature or outgoing long-wave radiation (OLR) are simulated by only a few GCMs. The GCMs that simulate a negative OLR - �a relationship show a strong positive correlation between �a and fcld. The short-wave total aerosol radiative forcing as simulated by the GCMs is strongly influenced by the simulated anthropogenic fraction of �a, and parameterisation assumptions such as a lower bound on Nd . Nevertheless, the strengths of the statistical relationships are good predictors for the aerosol forcings in the models. An estimate of the total short-wave aerosol forcing inferred from the combination of these predictors for the modelled forcings with the satellite-derived statistical relationships yields a global annual mean value of −1.5±0.5Wm−2. In an alternative approach, the radiative flux perturbation due to anthropogenic aerosols can be broken down into a component over the cloud-free portion of the globe (approximately the aerosol direct effect) and a component over the cloudy portion of the globe (approximately the aerosol indirect effect). An estimate obtained by scaling these simulated clearand cloudy-sky forcings with estimates of anthropogenic �a and satellite-retrieved Nd–�a regression slopes, respectively, yields a global, annual-mean aerosol direct effect estimate of −0.4±0.2Wm−2 and a cloudy-sky (aerosol indirect effect) estimate of −0.7±0.5Wm−2, with a total estimate of −1.2±0.4Wm−2.

The statistical downscaling model-decision centric (SDSM-DC): conceptual basis and applications

Regional climate downscaling has arrived at an important juncture. Some in the research community favour continued refinement and evaluation of downscaling techniques within a broader framework of uncertainty characterisation and reduction. Others are calling for smarter use of downscaling tools, accepting that conventional, scenario-led strategies for adaptation planning have limited utility in practice. This paper sets out the rationale and new functionality of the Decision Centric (DC) version of the Statistical DownScaling Model (SDSM-DC). This tool enables synthesis of plausible daily weather series, exotic variables (such as tidal surge), and climate change scenarios guided, not determined, by climate model output. Two worked examples are presented. The first shows how SDSM-DC can be used to reconstruct and in-fill missing records based on calibrated predictor-predictand relationships. Daily temperature and precipitation series from sites in Africa, Asia and North America are deliberately degraded to show that SDSM-DC can reconstitute lost data. The second demonstrates the application of the new scenario generator for stress testing a specific adaptation decision. SDSM-DC is used to generate daily precipitation scenarios to simulate winter flooding in the Boyne catchment, Ireland. This sensitivity analysis reveals the conditions under which existing precautionary allowances for climate change might be insufficient. We conclude by discussing the wider implications of the proposed approach and research opportunities presented by the new tool.

Calibration and evaluation of individual-based models using Approximate Bayesian Computation

This paper investigates the feasibility of using approximate Bayesian computation (ABC) to calibrate and evaluate complex individual-based models (IBMs). As ABC evolves, various versions are emerging, but here we only explore the most accessible version, rejection-ABC. Rejection-ABC involves running models a large number of times, with parameters drawn randomly from their prior distributions, and then retaining the simulations closest to the observations. Although well-established in some fields, whether ABC will work with ecological IBMs is still uncertain. Rejection-ABC was applied to an existing 14-parameter earthworm energy budget IBM for which the available data consist of body mass growth and cocoon production in four experiments. ABC was able to narrow the posterior distributions of seven parameters, estimating credible intervals for each. ABC’s accepted values produced slightly better fits than literature values do. The accuracy of the analysis was assessed using cross-validation and coverage, currently the best available tests. Of the seven unnarrowed parameters, ABC revealed that three were correlated with other parameters, while the remaining four were found to be not estimable given the data available. It is often desirable to compare models to see whether all component modules are necessary. Here we used ABC model selection to compare the full model with a simplified version which removed the earthworm’s movement and much of the energy budget. We are able to show that inclusion of the energy budget is necessary for a good fit to the data. We show how our methodology can inform future modelling cycles, and briefly discuss how more advanced versions of ABC may be applicable to IBMs. We conclude that ABC has the potential to represent uncertainty in model structure, parameters and predictions, and to embed the often complex process of optimizing an IBM’s structure and parameters within an established statistical framework, thereby making the process more transparent and objective.

Evaluation of some metals in Brazilian coffees cultivated during the process of conversion from conventional to organic agriculture

The aim of this study was to evaluate the presence of nutrients and toxic elements in coffees cultivated during the process of conversion, on organic agriculture, in southwest Bahia, Brazil. Levels of the nutrients and toxic elements were determined in samples of soils and coffee tissues from two transitional organic farms by atomic absorption spectrometry (FAAS). The metals in soil samples were extracted by Mehlich1 and USEPA-3050 procedures. Coffee samples from both farms presented relatively high levels of Cd, Zn and Cu (0.75,45.4 and 14.9 mu g g(-1). respectively), but were still below the limits specified by the Brazilian Food Legislation. The application of statistical methods showed that this finding can be attributed to the addition of high amounts of organic matter during the flowering tree period which can act on the bioavailability of metal ions in soils. (C) 2009 Elsevier Ltd. All rights reserved.

Histological evaluation of chitosan-based biomaterials used for the correction of critical size defects in rat`s calvaria

Chitosan, a biopolymer obtained from chitin, and its derivates, such as chitosan hydrochloride, has been reported as wound healing accelerators and as possible bone substitutes for tissue engineering, and therefore these Substances could be relevant in dentistry and periodontology. The purpose of this investigation was to make a histological evaluation of chitosan and chitosan hydrochloride biomaterials (gels) used in the correction of critical size bone defects made in rat`s calvaria. Bone defects of 8 mm in diameter were surgically created in the calviria of 50 Holtzman (Rattus norvegicus) rats and filled with blood clot (control), low molecular weight chitosan, high molecular weight chitosan, low molecular weight chitosan hydrochloride, and high molecular weight chitosan hydrochloride, numbering 10 animals, divided into two experimental periods (15 and 60 days), for each biomaterial. The histological evaluation was made based on the morphology of the new-formed tissues in defect`s region, and the results indicated that there was no statistical difference between the groups when the new bone formation in the entire defect`s area were compared (p > 0.05) and, except in the control groups, assorted degrees of inflammation Could be Seen. In Conclusion, chitosan and chitosan hydrochloride biomaterials used in this study were not able to promote new bone formation in critical size defects made in rat`s calvaria. (C) 2009 Wiley Periodicals, Inc. J Biomed Mater Res 93A: 107-114, 2016

QoS Evaluation of BandwidthSchedulers in IPTV Networks OfferedSRD Fluid Video Traffic

Internet protocol TV (IPTV) is predicted to be the key technology winner in the future. Efforts to accelerate the deployment of IPTV centralized model which is combined of VHO, encoders, controller, access network and Home network. Regardless of whether the network is delivering live TV, VOD, or Time-shift TV, all content and network traffic resulting from subscriber requests must traverse the entire network from the super-headend all the way to each subscriber's Set-Top Box (STB).IPTV services require very stringent QoS guarantees When IPTV traffic shares the network resources with other traffic like data and voice, how to ensure their QoS and efficiently utilize the network resources is a key and challenging issue. For QoS measured in the network-centric terms of delay jitter, packet losses and bounds on delay. The main focus of this thesis is on the optimized bandwidth allocation and smooth datatransmission. The proposed traffic model for smooth delivering video service IPTV network with its QoS performance evaluation. According to Maglaris et al [5] First, analyze the coding bit rate of a single video source. Various statistical quantities are derived from bit rate data collected with a conditional replenishment inter frame coding scheme. Two correlated Markov process models (one in discrete time and one incontinuous time) are shown to fit the experimental data and are used to model the input rates of several independent sources into a statistical multiplexer. Preventive control mechanism which is to be include CAC, traffic policing used for traffic control.QoS has been evaluated of common bandwidth scheduler( FIFO) by use fluid models with Markovian queuing method and analysis the result by using simulator andanalytically, Which is measured the performance of the packet loss, overflow and mean waiting time among the network users.

Design/Evaluation of A Methodology For Performance Optimization Of Indexable Carbide Inserts

In this project, two broad facets in the design of a methodology for performance optimization of indexable carbide inserts were examined. They were physical destructive testing and software simulation.For the physical testing, statistical research techniques were used for the design of the methodology. A five step method which began with Problem definition, through System identification, Statistical model formation, Data collection and Statistical analyses and results was indepthly elaborated upon. Set-up and execution of an experiment with a compression machine together with roadblocks and possible solution to curb road blocks to quality data collection were examined. 2k factorial design was illustrated and recommended for process improvement. Instances of first-order and second-order response surface analyses were encountered. In the case of curvature, test for curvature significance with center point analysis was recommended. Process optimization with method of steepest ascent and central composite design or process robustness studies of response surface analyses were also recommended.For the simulation test, AdvantEdge program was identified as the most used software for tool development. Challenges to the efficient application of this software were identified and possible solutions proposed. In conclusion, software simulation and physical testing were recommended to meet the objective of the project.

QoS evaluation of Bandwidth Schedulers in IPTV Networks Offered SRD Fluid Video Traffic

Internet protocol TV (IPTV) is predicted to be the key technology winner in the future. Efforts to accelerate the deployment of IPTV centralized model which is combined of VHO, encoders, controller, access network and Home network. Regardless of whether the network is delivering live TV, VOD, or Time-shift TV, all content and network traffic resulting from subscriber requests must traverse the entire network from the super-headend all the way to each subscriber's Set-Top Box (STB). IPTV services require very stringent QoS guarantees When IPTV traffic shares the network resources with other traffic like data and voice, how to ensure their QoS and efficiently utilize the network resources is a key and challenging issue. For QoS measured in the network-centric terms of delay jitter, packet losses and bounds on delay. The main focus of this thesis is on the optimized bandwidth allocation and smooth data transmission. The proposed traffic model for smooth delivering video service IPTV network with its QoS performance evaluation. According to Maglaris et al [5] first, analyze the coding bit rate of a single video source. Various statistical quantities are derived from bit rate data collected with a conditional replenishment inter frame coding scheme. Two correlated Markov process models (one in discrete time and one in continuous time) are shown to fit the experimental data and are used to model the input rates of several independent sources into a statistical multiplexer. Preventive control mechanism which is to be including CAC, traffic policing used for traffic control. QoS has been evaluated of common bandwidth scheduler( FIFO) by use fluid models with Markovian queuing method and analysis the result by using simulator and analytically, Which is measured the performance of the packet loss, overflow and mean waiting time among the network users.

Recent developments in statistical methods for detecting genetic loci affecting phenotypic variability

A number of recent works have introduced statistical methods for detecting genetic loci that affect phenotypic variability, which we refer to as variability-controlling quantitative trait loci (vQTL). These are genetic variants whose allelic state predicts how much phenotype values will vary about their expected means. Such loci are of great potential interest in both human and non-human genetic studies, one reason being that a detected vQTL could represent a previously undetected interaction with other genes or environmental factors. The simultaneous publication of these new methods in different journals has in many cases precluded opportunity for comparison. We survey some of these methods, the respective trade-offs they imply, and the connections between them. The methods fall into three main groups: classical non-parametric, fully parametric, and semi-parametric two-stage approximations. Choosing between alternatives involves balancing the need for robustness, flexibility, and speed. For each method, we identify important assumptions and limitations, including those of practical importance, such as their scope for including covariates and random effects. We show in simulations that both parametric methods and their semi-parametric approximations can give elevated false positive rates when they ignore mean-variance relationships intrinsic to the data generation process. We conclude that choice of method depends on the trait distribution, the need to include non-genetic covariates, and the population size and structure, coupled with a critical evaluation of how these fit with the assumptions of the statistical model.

Volatility modelling in the forex market: an empirical evaluation

We compare three frequently used volatility modelling techniques: GARCH, Markovian switching and cumulative daily volatility models. Our primary goal is to highlight a practical and systematic way to measure the relative effectiveness of these techniques. Evaluation comprises the analysis of the validity of the statistical requirements of the various models and their performance in simple options hedging strategies. The latter puts them to test in a "real life" application. Though there was not much difference between the three techniques, a tendency in favour of the cumulative daily volatility estimates, based on tick data, seems dear. As the improvement is not very big, the message for the practitioner - out of the restricted evidence of our experiment - is that he will probably not be losing much if working with the Markovian switching method. This highlights that, in terms of volatility estimation, no clear winner exists among the more sophisticated techniques.