Biobanks in oncology: global experience and Russian reality

One of the integral components of modern large-scale research projects in the field of medicine are biobanks. The main objective of this infrastructure is the professional collection of biological samples that can be studied with respect to a wide range of molecular biological parameters and will not lose their information value over a long storage period. These samples are made informative not only by correctly conducted preanalytical preparation at the stage of taking samples and placing them in storage, but also by detailed information support (the so-called annotated samples). The sample annotation is the fully collected personal, clinical and laboratory data about a patient. An important point of the biobank infrastructure is compliance with regulatory legal acts and ethical standards, including the procedure for signing an informed consent by a patient about voluntary donation of biological samples and the use of personal data. All this ensures the implementation of the main objective of creating biobanks the wide and uninterrupted availability of collections of biological material for researchers and developers and compliance with specific scientific tasks. This review is devoted to biobanking issues, as well as to the description and analysis of the currently existing oncological biobank infrastructure, both globally and within the Russian Federation.

ExploreModelMatrix: Interactive exploration for improved understanding of design matrices and linear models in R

Linear and generalized linear models are used extensively in many scientific fields, to model observed data and as the basis for hypothesis tests. The use of such models requires specification of a design matrix, and subsequent formulation of contrasts representing scientific hypotheses of interest. Proper execution of these steps requires a thorough understanding of the meaning of the individual coefficients, and is a frequent source of uncertainty for end users. Here, we present an R/Bioconductor package, ExploreModelMatrix, which enables interactive exploration of design matrices and linear model diagnostics. Given a sample annotation table and a desired design formula, the package displays how the model coefficients are combined to give the fitted values for each combination of predictor variables, which allows users to both extract the interpretation of each individual coefficient, and formulate desired linear contrasts. In addition, the interactive interface displays informative characteristics for the regular linear model corresponding to the provided design, such as variance inflation factors and the pseudoinverse of the design matrix.

Indoor Localization Based on Weighted Surfacing from Crowdsourced Samples

Fingerprinting-based indoor localization suffers from its time-consuming and labor-intensive site survey. As a promising solution, sample crowdsourcing has been recently promoted to exploit casually collected samples for building offline fingerprint database. However, crowdsourced samples may be annotated with erroneous locations, which raises a serious question about whether they are reliable for database construction. In this paper, we propose a cross-domain cluster intersection algorithm to weight each sample reliability. We then select those samples with higher weight to construct radio propagation surfaces by fitting polynomial functions. Furthermore, we employ an entropy-like measure to weight constructed surfaces for quantifying their different subarea consistencies and location discriminations in online positioning. Field measurements and experiments show that the proposed scheme can achieve high localization accuracy by well dealing with the sample annotation error and nonuniform density challenges.

Specificity of the number of nouns in Czech and its annotation in Prague Dependency Treebank

Specificity of the number of nouns in Czech and its annotation in Prague Dependency Treebank The paper focuses on the way how the grammatical category of number of nouns will be annotated in the forthcoming version of Prague Dependency Treebank (PDT 3.0), concentrating on the peculiarities beyond the regular opposition of singular and plural. A new semantic feature closely related to the category of number (so-called pair/group meaning) was introduced. Nouns such as ruce ‘hands’ or klíče ‘keys’ refer with their plural forms to a pair or to a typical group even more often than to a larger amount of single entities. Since pairs or groups can be referred to with most Czech concrete nouns, the pair/group meaning is considered as a grammaticalized meaning of nouns in Czech. In the present paper, manual annotation of the pair/group meaning is described, which was carried out on the data of Prague Dependency Treebank. A comparison with a sample annotation of data from Prague Dependency Treebank of Spoken Czech has demonstrated that the pair/group meaning is both more frequent and more easily distinguishable in the spoken than in the written data.