A web server for interactive and zoomable Chaos Game Representation images

Chaos Game Representation (CGR) is a generalized scale-independent Markov transition table, which is useful for the visualization and comparative study of genomic signature, or for the study of characteristic sequence motifs. However, in order to fully utilize the scale-independent properties of CGR, it should be accessible through scale-independent user interface instead of static images. Here we describe a web server and Perl library for generating zoomable CGR images utilizing Google Maps API, which is also easily searchable for specific motifs. The web server is freely accessible at , and the Perl library as well as the source code is distributed with the G-language Genome Analysis Environment under GNU General Public License

Modular Acquisition and Stimulation System for Timestamp-Driven Neuroscience Experiments

Dedicated systems are fundamental for neuroscience experimental protocols that require timing determinism and synchronous stimuli generation. We developed a data acquisition and stimuli generator system for neuroscience research, optimized for recording timestamps from up to 6 spiking neurons and entirely specified in a high-level Hardware Description Language (HDL). Despite the logic complexity penalty of synthesizing from such a language, it was possible to implement our design in a low-cost small reconfigurable device. Under a modular framework, we explored two different memory arbitration schemes for our system, evaluating both their logic element usage and resilience to input activity bursts. One of them was designed with a decoupled and latency insensitive approach, allowing for easier code reuse, while the other adopted a centralized scheme, constructed specifically for our application. The usage of a high-level HDL allowed straightforward and stepwise code modifications to transform one architecture into the other. The achieved modularity is very useful for rapidly prototyping novel electronic instrumentation systems tailored to scientific research.Comment: Preprint submitted to ARC 2015. Extended: 16 pages, 10 figures. The final publication is available at link.springer.co

Biological sequences as pictures – a generic two dimensional solution for iterated maps

<p>Abstract</p> <p>Background</p> <p>Representing symbolic sequences graphically using iterated maps has enjoyed an enduring popularity since it was first proposed in Jeffrey 1990 as chaos game representation (CGR). The usefulness of this representation goes beyond the convenience of a scale independent representation. It provides a variable memory length representation of transition. This includes the representation of succession with non-integer order, which comes with the promise of generalizing Markovian formalisms. The original proposal targeted genomic sequences only but since then several generalizations have been proposed, many specifically designed to handle protein data.</p> <p>Results</p> <p>The challenge of a general solution is that of deriving a bijective transformation of symbolic sequences into bi-dimensional planes. More specifically, it requires the regular fractal nesting of polygons. A first attempt at a general solution was proposed by Fiser 1994 by using non-overlapping circles that contain the polygons. This was used as a starting point to identify a more efficient solution where the encapsulating circles can overlap without the same happening for the sequence maps which are circumscribed to fractal polygon domains.</p> <p>Conclusion</p> <p>We identified the optimal inscribed packing solution for iterated maps of any Biological sequence, indeed of any symbolic sequence. The new solution maintains the prized bijective mapping property and includes the Sierpinski triangle and the CGR square as particular solutions of the more encompassing formulation.</p

The Hanle Effect in 1D, 2D and 3D

This paper addresses the problem of scattering line polarization and the Hanle effect in one-dimensional (1D), two-dimensional (2D) and three-dimensional (3D) media for the case of a two-level model atom without lower-level polarization and assuming complete frequency redistribution. The theoretical framework chosen for its formulation is the QED theory of Landi Degl'Innocenti (1983), which specifies the excitation state of the atoms in terms of the irreducible tensor components of the atomic density matrix. The self-consistent values of these density-matrix elements is to be determined by solving jointly the kinetic and radiative transfer equations for the Stokes parameters. We show how to achieve this by generalizing to Non-LTE polarization transfer the Jacobi-based ALI method of Olson et al. (1986) and the iterative schemes based on Gauss-Seidel iteration of Trujillo Bueno and Fabiani Bendicho (1995). These methods essentially maintain the simplicity of the Lambda-iteration method, but their convergence rate is extremely high. Finally, some 1D and 2D model calculations are presented that illustrate the effect of horizontal atmospheric inhomogeneities on magnetic and non-magnetic resonance line polarization signals.Comment: 14 pages and 5 figure

Quantum networks reveal quantum nonlocality

The results of local measurements on some composite quantum systems cannot be reproduced classically. This impossibility, known as quantum nonlocality, represents a milestone in the foundations of quantum theory. Quantum nonlocality is also a valuable resource for information processing tasks, e.g. quantum communication, quantum key distribution, quantum state estimation, or randomness extraction. Still, deciding if a quantum state is nonlocal remains a challenging problem. Here we introduce a novel approach to this question: we study the nonlocal properties of quantum states when distributed and measured in networks. Using our framework, we show how any one-way entanglement distillable state leads to nonlocal correlations. Then, we prove that nonlocality is a non-additive resource, which can be activated. There exist states, local at the single-copy level, that become nonlocal when taking several copies of it. Our results imply that the nonlocality of quantum states strongly depends on the measurement context.Comment: 4 + 3 pages, 4 figure

AGUIA: autonomous graphical user interface assembly for clinical trials semantic data services

<p>Abstract</p> <p>Background</p> <p>AGUIA is a front-end web application originally developed to manage clinical, demographic and biomolecular patient data collected during clinical trials at MD Anderson Cancer Center. The diversity of methods involved in patient screening and sample processing generates a variety of data types that require a resource-oriented architecture to capture the associations between the heterogeneous data elements. AGUIA uses a semantic web formalism, resource description framework (RDF), and a bottom-up design of knowledge bases that employ the S3DB tool as the starting point for the client's interface assembly.</p> <p>Methods</p> <p>The data web service, S3DB, meets the necessary requirements of generating the RDF and of explicitly distinguishing the description of the domain from its instantiation, while allowing for continuous editing of both. Furthermore, it uses an HTTP-REST protocol, has a SPARQL endpoint, and has open source availability in the public domain, which facilitates the development and dissemination of this application. However, S3DB alone does not address the issue of representing content in a form that makes sense for domain experts.</p> <p>Results</p> <p>We identified an autonomous set of descriptors, the GBox, that provides user and domain specifications for the graphical user interface. This was achieved by identifying a formalism that makes use of an RDF schema to enable the automatic assembly of graphical user interfaces in a meaningful manner while using only resources native to the client web browser (JavaScript interpreter, document object model). We defined a generalized RDF model such that changes in the graphic descriptors are automatically and immediately (locally) reflected into the configuration of the client's interface application.</p> <p>Conclusions</p> <p>The design patterns identified for the GBox benefit from and reflect the specific requirements of interacting with data generated by clinical trials, and they contain clues for a general purpose solution to the challenge of having interfaces automatically assembled for multiple and volatile views of a domain. By coding AGUIA in JavaScript, for which all browsers include a native interpreter, a solution was found that assembles interfaces that are meaningful to the particular user, and which are also ubiquitous and lightweight, allowing the computational load to be carried by the client's machine.</p

Browser-based Data Annotation, Active Learning, and Real-Time Distribution of Artificial Intelligence Models: From Tumor Tissue Microarrays to COVID-19 Radiology.

BACKGROUND: Artificial intelligence (AI) is fast becoming the tool of choice for scalable and reliable analysis of medical images. However, constraints in sharing medical data outside the institutional or geographical space, as well as difficulties in getting AI models and modeling platforms to work across different environments, have led to a "reproducibility crisis" in digital medicine. METHODS: This study details the implementation of a web platform that can be used to mitigate these challenges by orchestrating a digital pathology AI pipeline, from raw data to model inference, entirely on the local machine. We discuss how this federated platform provides governed access to data by consuming the Application Program Interfaces exposed by cloud storage services, allows the addition of user-defined annotations, facilitates active learning for training models iteratively, and provides model inference computed directly in the web browser at practically zero cost. The latter is of particular relevance to clinical workflows because the code, including the AI model, travels to the user's data, which stays private to the governance domain where it was acquired. RESULTS: We demonstrate that the web browser can be a means of democratizing AI and advancing data socialization in medical imaging backed by consumer-facing cloud infrastructure such as Box.com. As a case study, we test the accompanying platform end-to-end on a large dataset of digital breast cancer tissue microarray core images. We also showcase how it can be applied in contexts separate from digital pathology by applying it to a radiology dataset containing COVID-19 computed tomography images. CONCLUSIONS: The platform described in this report resolves the challenges to the findable, accessible, interoperable, reusable stewardship of data and AI models by integrating with cloud storage to maintain user-centric governance over the data. It also enables distributed, federated computation for AI inference over those data and proves the viability of client-side AI in medical imaging. AVAILABILITY: The open-source application is publicly available at , with a short video demonstration at

Evolutionary plasticity determination by orthologous groups distribution

<p>Abstract</p> <p>Background</p> <p>Genetic plasticity may be understood as the ability of a functional gene network to tolerate alterations in its components or structure. Usually, the studies involving gene modifications in the course of the evolution are concerned to nucleotide sequence alterations in closely related species. However, the analysis of large scale data about the distribution of gene families in non-exclusively closely related species can provide insights on how plastic or how conserved a given gene family is. Here, we analyze the abundance and diversity of all Eukaryotic Clusters of Orthologous Groups (KOG) present in STRING database, resulting in a total of 4,850 KOGs. This dataset comprises 481,421 proteins distributed among 55 eukaryotes.</p> <p>Results</p> <p>We propose an index to evaluate the evolutionary plasticity and conservation of an orthologous group based on its abundance and diversity across eukaryotes. To further KOG plasticity analysis, we estimate the evolutionary distance average among all proteins which take part in the same orthologous group. As a result, we found a strong correlation between the evolutionary distance average and the proposed evolutionary plasticity index. Additionally, we found low evolutionary plasticity in <it>Saccharomyces cerevisiae </it>genes associated with inviability and <it>Mus musculus </it>genes associated with early lethality. At last, we plot the evolutionary plasticity value in different gene networks from yeast and humans. As a result, it was possible to discriminate among higher and lower plastic areas of the gene networks analyzed.</p> <p>Conclusions</p> <p>The distribution of gene families brings valuable information on evolutionary plasticity which might be related with genetic plasticity. Accordingly, it is possible to discriminate among conserved and plastic orthologous groups by evaluating their abundance and diversity across eukaryotes.</p> <p>Reviewers</p> <p>This article was reviewed by Prof Manyuan Long, Hiroyuki Toh, and Sebastien Halary.</p

Education and inequality in Finland, Spain and Brazil

Production of INCASI Project H2020-MSCA-RISE-2015 GA 691004Finland, Spain and Brazil are three very internally complex and heterogeneous realities, with contradictions and permanent reforms to their education systems. In a first quantitative approach each country can be placed in a continuum of the education system that goes from most successful in terms of reaching a high level of education all across the population, in conditions of equity and facilitating youths' incorporation into the labour market, to least successful, with Finland and Brazil occupying either end of the spectrum respectively and Spain occupying an intermediate situation. Although there are differences, they share certain tensions in their respective education systems. On the one hand, about the conception of education, ranging from more utilitarian, human capital theories, to the more humanist and civic-minded perspective. On the other hand, the challenge of comprehensiveness between an academic and a vocational path. In addition, there is also the challenge of improving the education level of the population while also improving equality. The tensions differ from country to country, since their education traditions and cooperation and conflict strategies between the education agents, with varying levels of resources and different alliances with political actors vary, as does the social consensus