Combining dense and sparse labeling in optical DNA mapping

Optical DNA mapping (ODM) is based on fluorescent labeling, stretching and imaging of single DNA molecules to obtain sequence-specific fluorescence profiles, DNA barcodes. These barcodes can be mapped to theoretical counterparts obtained from DNA reference sequences, which in turn allow for DNA identification in complex samples and for detecting structural changes in individual DNA molecules. There are several types of DNA labeling schemes for ODM and for each labeling type one or several types of match scoring methods are used. By combining the information from multiple labeling schemes one can potentially improve mapping confidence; however, combining match scores from different labeling assays has not been implemented yet. In this study, we introduce two theoretical methods for dealing with analysis of DNA molecules with multiple label types. In our first method, we convert the alignment scores, given as output from the different assays, into p-values using carefully crafted null models. We then combine the p-values for different label types using standard methods to obtain a combined match score and an associated combined p-value. In the second method, we use a block bootstrap approach to check for the uniqueness of a match to a database for all barcodes matching with a combined p-value below a predefined threshold. For obtaining experimental dual-labeled DNA barcodes, we introduce a novel assay where we cut plasmid DNA molecules from bacteria with restriction enzymes and the cut sites serve as sequence-specific markers, which together with barcodes obtained using the established competitive binding labeling method, form a dual-labeled barcode. All experimental data in this study originates from this assay, but we point out that our theoretical framework can be used to combine data from all kinds of available optical DNA mapping assays. We test our multiple labeling frameworks on barcodes from two different plasmids and synthetically generated barcodes (combined competitive-binding- and nick-labeling). It is demonstrated that by simultaneously using the information from all label types, we can substantially increase the significance when we match experimental barcodes to a database consisting of theoretical barcodes for all sequenced plasmids.

Introduction to local certification

A distributed graph algorithm is basically an algorithm where every node of a graph can look at its neighborhood at some distance in the graph and chose its output. As distributed environment are subject to faults, an important issue is to be able to check that the output is correct, or in general that the network is in proper configuration with respect to some predicate. One would like this checking to be very local, to avoid using too much resources. Unfortunately most predicates cannot be checked this way, and that is where certification comes into play. Local certification (also known as proof-labeling schemes, locally checkable proofs or distributed verification) consists in assigning labels to the nodes, that certify that the configuration is correct. There are several point of view on this topic: it can be seen as a part of self-stabilizing algorithms, as labeling problem, or as a non-deterministic distributed decision. This paper is an introduction to the domain of local certification, giving an overview of the history, the techniques and the current research directions.

Comparison of 12 Different Animal Welfare Labeling Schemes in the Pig Sector

Animal welfare labeling schemes have been developed to respond to consumers’ expectations regarding farm animal welfare. They are designed to certify that labeled products comply with certain animal welfare standards. In this study, 12 pig welfare labeling schemes were reviewed, and their criteria related to pig welfare were compared. Information regarding farrowing criteria, space allowance, outdoor access, mutilations, and provision of enrichments and bedding material were gathered from the labels’ internet pages and documentation. The results indicated a substantial variation between the labels in terms of the level of animal welfare they ensure. While certain schemes barely exceeded the minimum standards for the protection of pigs in the European Union, more demanding tiers of the multitier schemes had the potential to improve animal welfare substantially. The most ambitious tiers of multistage schemes were often comparable to organic standards providing outdoor facilities and additional space. The heterogeneity of the labels’ standards complicates the comparison of labels.

A New Approach to Solving the Problem of Generating Sets of Complex Structural Objects Based on a Quasi-Equivalent Transformation of a Labeling Scheme

The paper presents the results of a theoretical study related to the development of methods for constructing generating structures based on labeling schemes for generating sets of complex structural objects. In a theoretical aspect, generated objects are mappings of sets of objects into a set of labels, and in practical terms, they can be, in particular, visual images. The scientific and practical interest in generative constructions is that they can be used to determine whether objects belong to a certain class, that is, to solve the problem of pattern recognition. The problem of constructing generating labeling scheme belongs to a wide section of modern applied informatics that embraces Constraint Satisfaction Problem and related themes [1–4]. But this problem has not been posed before and there are still no regular methods for solving it. The analysis of the above methods is based on the formalism of the consistent labeling problem [6, 10, 11], which is, on the one hand, a generalization of many statements of discrete problems of Constraint Satisfaction, and, on the other hand, a transparent theoretical construction with a well-developed mathematical foundation. The problem of constructing a relational scheme (in this case, labeling scheme) that generates a given set of mappings, by analogy with linguistic models, may be named “the problem of grammar restoration” [12–14]. In previous studies it was shown that to solve this problem it makes sense to use equivalent transformations of the labeling scheme [11]. This is because the source table listing all the complex objects that should be generated by the target scheme is itself a trivial variant of the scheme with a given set of consistent labelings. This means that the source scheme and target scheme are equivalent. However, one of the equivalent operations – disunion of a column – cannot be used regularly, since it requires certain conditions to be met regarding the internal structure of the column. In this case, to expand the capabilities of four known equivalent transformations of the labeling scheme – deleting and appending nonexistent labeling, as well as joining of columns and column disunion – a non-equivalent transformation was added – "coloring the column labelings". The purpose of the paper is to introduce and investigate operation of "coloring the column labelings" that leads to a non-equivalent transformation of a labeling scheme. Show the advisability of using the known equivalent and the introduced quasi-equivalent transformations of the labeling scheme to solve the problem of constructing generating structures based on labeling schemes. Results. The transformation of the labeling scheme, called "coloring the labelings of the scheme column", has been introduced. It is shown that its implementation leads to a quasi-equivalent labeling scheme, by solving which it is possible to uniquely restore the solution of the original problem. A method is proposed for using the newly introduced operation to transform the labeling scheme into a quasi-equivalent labeling scheme, in which it becomes possible to regularly perform the column decoupling operation. This ability of the operation of "coloring the column labelings" opens the way to the creation of a method for solving the problem of restoring a labeling scheme that generates a given set of consistent labelings. Keywords: relational scheme, consistent labeling scheme, equivalent labeling scheme transformations, constraint satisfaction problem.

A Bibliometric Analysis of Carbon Labeling Schemes in the Period 2007–2019

Carbon labeling schemes enable consumers to be aware of carbon emissions regarding products or services, to help change their purchasing behaviors. This study provides a bibliometric analysis to review the research progress of carbon labeling schemes during the period 2007–2019, in order to provide insight into its future development. Number of publications, countries of publications, authors, institutions, and highly cited papers are included for statistical analysis. The CiteSpace software package is used to visualize the national collaboration, keywords co-appearance, and aggregation. The results are given as follows: (1) there are 175 articles published in the pre-defined period, which shows a gradual increase, with a peak occurred in 2016; (2) carbon labeling schemes are mainly applied to grocery products, and gradually emerged in construction and tourism. (3) Existing studies mainly focus on examination of utility of carbon labeling schemes, by conducting surveys to investigate individual perception, preference, and willingness to pay. (4) Future research will include the optimization of life cycle assessment for labeling accreditation, improvement of labeling visualization for better expression, and normalization of various environmental labels to promote sustainable consumption.