Hot-spot based examination of immunohistochemically stained histological specimens is one of the most important procedures in pathomorphological practice. The development of image acquisition equipment and computational units allows for the automation of this process. Moreover, a lot of possible technical problems occur in everyday histological material, which increases the complexity of the problem. Thus, a full context-based analysis of histological specimens is also needed in the quantification of immunohistochemically stained specimens. One of the most important reactions is the Ki-67 proliferation marker in meningiomas, the most frequent intracranial tumour. The aim of our study is to propose a context-based analysis of Ki-67 stained specimens of meningiomas for automatic selection of hot-spots. The proposed solution is based on textural analysis, mathematical morphology, feature ranking and classification, as well as on the proposed hot-spot gradual extinction algorithm to allow for the proper detection of a set of hot-spot fields. The designed whole slide image processing scheme eliminates such artifacts as hemorrhages, folds or stained vessels from the region of interest. To validate automatic results, a set of 104 meningioma specimens were selected and twenty hot-spots inside them were identified independently by two experts. The Spearman rho correlation coefficient was used to compare the results which were also analyzed with the help of a Bland-Altman plot. The results show that most of the cases (84) were automatically examined properly with two fields of view with a technical problem at the very most. Next, 13 had three such fields, and only seven specimens did not meet the requirement for the automatic examination. Generally, the Automatic System identifies hot-spot areas, especially their maximum points, better. Analysis of the results confirms the very high concordance between an automatic Ki-67 examination and the expert's results, with a Spearman
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The Australian Dark Energy Survey (OzDES) is a 100-night spectroscopic survey underway on the Anglo-Australian Telescope using the fibre-fed 2-degree-field (2dF) spectrograph. We have developed a new redshifting application MARZ with greater usability, flexibility, and the capacity to analyse a wider range of object types than the RUNZ software package previously used for redshifting spectra from 2dF. MARZ is an open-source, client-based, Javascript web-application which provides an intuitive interface and powerful automatic matching capabilities on spectra generated from the AAOmega spectrograph to produce high quality spectroscopic redshift measurements. The software can be run interactively or via the command line, and is easily adaptable to other instruments and pipelines if conforming to the current FITS file standard is not possible. Behind the scenes, a modified version of the AUTOZ cross-correlation algorithm is used to match input spectra against a variety of stellar and galaxy templates, and automatic matching performance for OzDES spectra has increased from 54% (RUNZ) to 91% (MARZ). Spectra not matched correctly by the automatic algorithm can be easily redshifted manually by cycling automatic results, manual template comparison, or marking spectral features.
Fourteen field campaigns were conducted in five inland lakes during different seasons between 2006 and 2013, and a total of 398 water samples with varying optical characteristics were collected. The characteristics were analyzed based on remote sensing reflectance, and an automatic cluster two-step method was applied for water classification. The inland waters could be clustered into three types, which we labeled water types I, II and III. From water types I to III, the effect of the phytoplankton on the optical characteristics gradually decreased. Four chlorophyll-a retrieval algorithms for Case II water, a two-band, three-band, four-band and SCI (Synthetic Chlorophyll Index) algorithm were evaluated for three water types based on the MERIS bands. Different MERIS bands were used for the three water types in each of the four algorithms. The four algorithms had different levels of retrieval accuracy for each water type, and no single algorithm could be successfully applied to all water types. For water types I and III, the three-band algorithm performed the best, while the four-band algorithm had the highest retrieval accuracy for water type II. However, the three-band algorithm is preferable to the two-band algorithm for turbid eutrophic inland waters. The SCI algorithm is recommended for highly turbid water with a higher concentration of total suspended solids. Our research indicates that the chlorophyll-a concentration retrieval by remote sensing for optically contrasted inland water requires a specific algorithm that is based on the optical characteristics of inland water bodies to obtain higher estimation accuracy. Copyright 2015 Elsevier B.V. All rights reserved.
Objective. Artifact reduction in electroencephalogram (EEG) signals is usually necessary to carry out data analysis appropriately. Despite the large amount of denoising techniques available with a multichannel setup, there is a lack of efficient algorithms that remove (not only detect) blink-artifacts from a single channel EEG, which is of interest in many clinical and research applications. This paper describes and evaluates the iterative template matching and suppression (ITMS), a new method proposed for detecting and suppressing the artifact associated with the blink activity from a single channel EEG. Approach. The approach of ITMS consists of (a) an iterative process in which blink-events are detected and the blink-artifact waveform of the analyzed subject is estimated, (b) generation of a signal modeling the blink-artifact, and (c) suppression of this signal from the raw EEG. The performance of ITMS is compared with the multi-window summation of derivatives within a window (MSDW) technique using both synthesized and real EEG data. Main results. Results suggest that ITMS presents an adequate performance in detecting and suppressing blink-artifacts from a single channel EEG. When applied to the analysis of cortical auditory evoked potentials (CAEPs), ITMS provides a significant quality improvement in the resulting responses, i.e. in a cohort of 30 adults, the mean correlation coefficient improved from 0.37 to 0.65 when the blink-artifacts were detected and suppressed by ITMS. Significance. ITMS is an efficient solution to the problem of denoising blink-artifacts in single-channel EEG applications, both in clinical and research fields. The proposed ITMS algorithm is stable; automatic, since it does not require human intervention; low-invasive, because the EEG segments not contaminated by blink-artifacts remain unaltered; and easy to implement, as can be observed in the Matlab script implemeting the algorithm provided as supporting material.
"Objective" methods to monitor physical activity and sedentary patterns in free-living conditions are necessary to further our understanding of their impacts on health. In recent years, many software solutions capable of automatically identifying activity types from portable accelerometry data have been developed, with promising results in controlled conditions, but virtually no reports on field tests. An automatic classification algorithm initially developed using laboratory-acquired data (59 subjects engaging in a set of 24 standardized activities) to discriminate between 8 activity classes (lying, slouching, sitting, standing, walking, running, and cycling) was applied to data collected in the field. Twenty volunteers equipped with a hip-worn triaxial accelerometer performed at their own pace an activity set that included, among others, activities such as walking the streets, running, cycling, and taking the bus. Performances of the laboratory-calibrated classification algorithm were compared with those of an alternative version of the same model including field-collected data in the learning set. Despite good results in laboratory conditions, the performances of the laboratory-calibrated algorithm (assessed by confusion matrices) decreased for several activities when applied to free-living data. Recalibrating the algorithm with data closer to real-life conditions and from an independent group of subjects proved useful, especially for the detection of sedentary behaviors while in transports, thereby improving the detection of overall sitting (sensitivity: laboratory model = 24.9%; recalibrated model = 95.7%). Automatic identification methods should be developed using data acquired in free-living conditions rather than data from standardized laboratory activity sets only, and their limits carefully tested before they are used in field studies. Copyright 2015 the American Physiological Society.
Computer-aided drug design has become an important component of the drug discovery process. Despite the advances in this field, there is not a unique modeling approach that can be successfully applied to solve the whole range of problems faced during QSAR modeling. Feature selection and ensemble modeling are active areas of research in ligand-based drug design. Here we introduce the GA(M)E-QSAR algorithm that combines the search and optimization capabilities of Genetic Algorithms with the simplicity of the Adaboost ensemble-based classification algorithm to solve binary classification problems. We also explore the usefulness of Meta-Ensembles trained with Adaboost and Voting schemes to further improve the accuracy, generalization, and robustness of the optimal Adaboost Single Ensemble derived from the Genetic Algorithm optimization. We evaluated the performance of our algorithm using five data sets from the literature and found that it is capable of yielding similar or better classification results to what has been reported for these data sets with a higher enrichment of active compounds relative to the whole actives subset when only the most active chemicals are considered. More important, we compared our methodology with state of the art feature selection and classification approaches and found that it can provide highly accurate, robust, and generalizable models. In the case of the Adaboost Ensembles derived from the Genetic Algorithm search, the final models are quite simple since they consist of a weighted sum of the output of single feature classifiers. Furthermore, the Adaboost scores can be used as ranking criterion to prioritize chemicals for synthesis and biological evaluation after virtual screening experiments. 2ff7e9595c
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