Consciousness transitions during epilepsy seizures through the lens of integrated information theory.

Consciousness is one of the most complex aspects of human experience. Studying the mechanisms involved in the transitions among different levels of consciousness remains as one of the greatest challenges in neuroscience. In this study we use a measure of integrated information (ΦAR) to evaluate dynamic changes during consciousness transitions. We applied the measure to intracranial electroencephalography (SEEG) recordings collected from 6 patients that suffer from refractory epilepsy, taking into account inter-ictal, pre-ictal and ictal periods. We analyzed the dynamical evolution of ΦAR in groups of electrode contacts outside the epileptogenic region and compared it with the Consciousness Seizure Scale (CCS). We show that changes on ΦAR are significantly correlated with changes in the reported states of consciousness.

The Missing Person problem through the lens of information theory.

Missing person cases typically require a genetic kinship test to determine the relationship between an unidentified individual and the relatives of the missing person. When not enough genetic evidence has been collected the lack of statistical power of these tests might lead to unreliable results. This is particularly true when just a few distant relatives are available for genotyping. In this contribution, we considered a Bayesian network approach for kinship testing and proposed several information theoretic metrics in order to quantitatively evaluate the information content of pedigrees. We show how these statistics are related to the widely used likelihood ratio values and could be employed to efficiently prioritize family members in order to optimize the statistical power in missing person problems. Our methodology seamlessly integrates with Bayesian modeling approaches, like the GENis platform that we have recently developed for high-throughput missing person identification tasks. Furthermore, our approach can also be easily incorporated into Elston-Stewart forensic frameworks. To facilitate the application of our methodology, we have developed the forensIT package, freely available on CRAN repository, which implements all the methodologies described in our manuscript.

Molecular Information Theory Meets Protein Folding.

We propose an application of molecular information theory to analyze the folding of single domain proteins. We analyze results from various areas of protein science, such as sequence-based potentials, reduced amino acid alphabets, backbone configurational entropy, secondary structure content, residue burial layers, and mutational studies of protein stability changes. We found that the average information contained in the sequences of evolved proteins is very close to the average information needed to specify a fold ∼2.2 ± 0.3 bits/(site·operation). The effective alphabet size in evolved proteins equals the effective number of conformations of a residue in the compact unfolded state at around 5. We calculated an energy-to-information conversion efficiency upon folding of around 50%, lower than the theoretical limit of 70%, but much higher than human-built macroscopic machines. We propose a simple mapping between molecular information theory and energy landscape theory and explore the connections between sequence evolution, configurational entropy, and the energetics of protein folding.

CeTF: an R/Bioconductor package for transcription factor co-expression networks using regulatory impact factors (RIF) and partial correlation and information (PCIT) analysis.

BACKGROUND: Finding meaningful gene-gene interaction and the main Transcription Factors (TFs) in co-expression networks is one of the most important challenges in gene expression data mining. RESULTS: Here, we developed the R package "CeTF" that integrates the Partial Correlation with Information Theory (PCIT) and Regulatory Impact Factors (RIF) algorithms applied to gene expression data from microarray, RNA-seq, or single-cell RNA-seq platforms. This approach allows identifying the transcription factors most likely to regulate a given network in different biological systems - for example, regulation of gene pathways in tumor stromal cells and tumor cells of the same tumor. This pipeline can be easily integrated into the high-throughput analysis. To demonstrate the CeTF package application, we analyzed gastric cancer RNA-seq data obtained from TCGA (The Cancer Genome Atlas) and found the HOXB3 gene as the second most relevant TFs with a high regulatory impact (TFs-HRi) regulating gene pathways in the cell cycle. CONCLUSION: This preliminary finding shows the potential of CeTF to list master regulators of gene networks. CeTF was designed as a user-friendly tool that provides many highly automated functions without requiring the user to perform many complicated processes. It is available on Bioconductor ( http://bioconductor.org/packages/CeTF ) and GitHub ( http://github.com/cbiagii/CeTF ).

Information theory inspired optimization algorithm for efficient service orchestration in distributed systems.

Distributed Systems architectures are becoming the standard computational model for processing and transportation of information, especially for Cloud Computing environments. The increase in demand for application processing and data management from enterprise and end-user workloads continues to move from a single-node client-server architecture to a distributed multitier design where data processing and transmission are segregated. Software development must considerer the orchestration required to provision its core components in order to deploy the services efficiently in many independent, loosely coupled-physically and virtually interconnected-data centers spread geographically, across the globe. This network routing challenge can be modeled as a variation of the Travelling Salesman Problem (TSP). This paper proposes a new optimization algorithm for optimum route selection using Algorithmic Information Theory. The Kelly criterion for a Shannon-Bernoulli process is used to generate a reliable quantitative algorithm to find a near optimal solution tour. The algorithm is then verified by comparing the results with benchmark heuristic solutions in 3 test cases. A statistical analysis is designed to measure the significance of the results between the algorithms and the entropy function can be derived from the distribution. The tested results shown an improvement in the solution quality by producing routes with smaller length and time requirements. The quality of the results proves the flexibility of the proposed algorithm for problems with different complexities without relying in nature-inspired models such as Genetic Algorithms, Ant Colony, Cross Entropy, Neural Networks, 2opt and Simulated Annealing. The proposed algorithm can be used by applications to deploy services across large cluster of nodes by making better decision in the route design. The findings in this paper unifies critical areas in Computer Science, Mathematics and Statistics that many researchers have not explored and provided a new interpretation that advances the understanding of the role of entropy in decision problems encoded in Turing Machines.

Dynamics in cortical activity revealed by resting-state MEG rhythms.

The brain is a biophysical system subject to information flows that may be thought of as a many-body architecture with a spatiotemporal dynamics described by its neuronal structures. The oscillatory nature of brain activity allows these structures (nodes) to be described as a set of coupled oscillators forming a network where the node dynamics and that of the network topology can be studied. Quantifying its dynamics at various scales is an issue that claims to be explored for several brain activities, e.g., activity at rest. The resting-state (RS) associates the underlying brain dynamics of healthy subjects that are not actively compromised with sensory or cognitive processes. Studying its dynamics is highly non-trivial but opens the door to understand the general principles of brain functioning, as well as to contrast a passive null condition vs the dynamics of pathologies or non-resting activities. Here, we hypothesize about how the spatiotemporal dynamics of cortical fluctuations could be for healthy subjects at RS. To do that, we retrieve the alphabet that reconstructs the dynamics (entropy-complexity) of magnetoencephalography (MEG) signals. We assemble the cortical connectivity to elicit the dynamics in the network topology. We depict an order relation between entropy and complexity for frequency bands that is ubiquitous for different temporal scales. We unveiled that the posterior cortex conglomerates nodes with both stronger dynamics and high clustering for α band. The existence of an order relation between dynamic properties suggests an emergent phenomenon characteristic of each band. Interestingly, we find the posterior cortex as a domain of dual character that plays a cardinal role in both the dynamics and structure regarding the activity at rest. To the best of our knowledge, this is the first study with MEG involving information theory and network science to better understand the dynamics and structure of brain activity at rest for different bands and scales.

Estimating ecoacoustic activity in the Amazon rainforest through Information Theory quantifiers.

Automatic monitoring of biodiversity by acoustic sensors has become an indispensable tool to assess environmental stress at an early stage. Due to the difficulty in recognizing the Amazon's high acoustic diversity and the large amounts of raw audio data recorded by the sensors, the labeling and manual inspection of this data is not feasible. Therefore, we propose an ecoacoustic index that allows us to quantify the complexity of an audio segment and correlate this measure with the biodiversity of the soundscape. The approach uses unsupervised methods to avoid the problem of labeling each species individually. The proposed index, named the Ecoacoustic Global Complexity Index (EGCI), makes use of Entropy, Divergence and Statistical Complexity. A distinguishing feature of this index is the mapping of each audio segment, including those of varied lengths, as a single point in a 2D-plane, supporting us in understanding the ecoacoustic dynamics of the rainforest. The main results show a regularity in the ecoacoustic richness of a floodplain, considering different temporal granularities, be it between hours of the day or between consecutive days of the monitoring program. We observed that this regularity does a good job of characterizing the soundscape of the environmental protection area of Mamirauá, in the Amazon, differentiating between species richness and environmental phenomena.

An information theory approach to biocultural complexity.

The study of biocultural diversity requires the use of appropriate concepts and analytical tools. Particularly, there is a need of indices capable to show the degree of stratification in the set of interactions among cultures and groups of plants and animals in a given region. Here, we present a mathematical approach based on the mutual Shannon information theory to study the relationships among cultural and biological groups. Biocultural complexity was described in terms of effective biocultural units, a new concept defined in this work. From the mathematical formulation of biocultural complexity, formulas were derived to measure the specificity of biological groups and the specialization of cultures, based on the association of human societies with plant or animal groups. To exemplify the concepts and tools, two data sets were analyzed; 1) a set that included artificial data in order to demonstrate the use of the formulas and calculate the indices, and 2) a set that included published data on the use of 18 mushroom species by people in five villages of eastern India. Analysis of the first data set revealed a clear case of biocultural complexity, whereas that of the second set showed that the villages and the use of biological resources composed a single biocultural unit. Overall, hypothesis testing of the association among cultures and biological species was consistent with the information that was provided by the new indices.

Phylogeography of the Variable Antshrike (Thamnophilus caerulescens), a South American passerine distributed along multiple environmental gradients.

The Neotropics show a wealth of distributional patterns shared by many co-distributed species. A distinctive pattern is the so-called "circum-Amazonian distribution," which is observed in species that do not occur in Amazonia but rather along a belt of forested habitats spanning south and east of Amazonia, the Andean foothills, and often into the Venezuelan Coastal Range and the Tepuis. Although this pattern is widespread across animals and plants, its underlying biogeographic mechanisms remain poorly understood. The Variable Antshrike (Thamnophilus caerulescens) is a sexually dimorphic suboscine passerine that exhibits extreme plumage variation and occurs along the southern portion of the circum-Amazonian belt. We describe broad-scale phylogeographic patterns of T. caerulescens and assess its demographic history using DNA sequences from the mitochondrion and ultraconserved elements (UCEs). We identified three genomic clusters: a) northern Atlantic Forest; b) southeastern Cerrado and central-southern Atlantic Forest, and c) Chaco and Andes. Our results were consistent with Pleistocene divergence followed by gene flow, mainly between the latter two clusters. There were no genetic signatures of rapid population expansions or bottlenecks. The population from the northern Atlantic Forest was the most genetically divergent group within the species. The demographic history of T. caerulescens was probably affected by series of humid and dry periods throughout the Quaternary that generated subtle population expansions and contractions allowing the intermittent connection of habitats along the circum-Amazonian belt. Recognizing the dynamic history of climate-mediated forest expansions, contractions, and connections during the South American Pleistocene is central toward a mechanistic understanding of circum-Amazonian distributions.

A Smartphone Lightweight Method for Human Activity Recognition Based on Information Theory.

Smartphones have emerged as a revolutionary technology for monitoring everyday life, and they have played an important role in Human Activity Recognition (HAR) due to its ubiquity. The sensors embedded in these devices allows recognizing human behaviors using machine learning techniques. However, not all solutions are feasible for implementation in smartphones, mainly because of its high computational cost. In this context, the proposed method, called HAR-SR, introduces information theory quantifiers as new features extracted from sensors data to create simple activity classification models, increasing in this way the efficiency in terms of computational cost. Three public databases (SHOAIB, UCI, WISDM) are used in the evaluation process. The results have shown that HAR-SR can classify activities with 93% accuracy when using a leave-one-subject-out cross-validation procedure (LOSO).

Communication efficiency of color naming across languages provides a new framework for the evolution of color terms.

Languages vary in their number of color terms. A widely accepted theory proposes that languages evolve, acquiring color terms in a stereotyped sequence. This theory, by Berlin and Kay (BK), is supported by analyzing best exemplars ("focal colors") of basic color terms in the World Color Survey (WCS) of 110 languages. But the instructions of the WCS were complex and the color chips confounded hue and saturation, which likely impacted focal-color selection. In addition, it is now known that even so-called early-stage languages nonetheless have a complete representation of color distributed across the population. These facts undermine the BK theory. Here we revisit the evolution of color terms using original color-naming data obtained with simple instructions in Tsimane', an Amazonian culture that has limited contact with industrialized society. We also collected data in Bolivian-Spanish speakers and English speakers. We discovered that information theory analysis of color-naming data was not influenced by color-chip saturation, which motivated a new analysis of the WCS data. Embedded within a universal pattern in which warm colors (reds, oranges) are always communicated more efficiently than cool colors (blues, greens), as languages increase in overall communicative efficiency about color, some colors undergo greater increases in communication efficiency compared to others. Communication efficiency increases first for yellow, then brown, then purple. The present analyses and results provide a new framework for understanding the evolution of color terms: what varies among cultures is not whether colors are seen differently, but the extent to which color is useful.

Information theory unveils the evolution of tRNA identity elements in the three domains of life.

We determined the identity elements of each tRNA isoacceptor for the three domains of life: Eubacteria, Archaea, and Eukarya. Our analyses encompass the most updated and curated available databases using an information theory approach. We obtained a collection of identity clusters for each of the isoacceptors of the 20 canonical amino acids for the three major domains of life. The identity clusters for all isoacceptors are compared within and among the three domains to determine their pattern of differentiation and to shed light on the evolution of the identity elements.

Apuntes sobre la evolución histórica de la obra de Pedro Ortiz Cabanillas y su teoría sociobiológica informacional / Notes on the historical evolution of the work of Pedro Ortiz Cabanillas and his sociobiological informational theory

RESUMEN La Teoría Sociobiológica Informacional propone una definición radicalmente distinta de los sistemas vivos, y con lo mismo es la única teoría neurológica existente que evade el problema mente-cerebro y que explica la naturaleza de la conciencia humana. Fue desarrollada por Pedro Ortiz Cabanillas entre 1984 y 2011. En este documento vamos a realizar un recuento de todas sus obras más importantes. Incluimos, adicionalmente, material inédito de los años 1998, 1999, 2006, y 2009.

ABSTRACT The Informational Sociobiological Theory proposes a radically-different definition of living systems and, therefore, is the only existing neurological theory that evades the mind-brain problem and explains the nature of human consciousness. It was developed by Pedro Ortiz Cabanillas between 1984 and 2011. In this document we are presenting a listing of his main works. We include, additionally, unpublished material of the years 1998, 1999, 2006, and 2009.

[Notes on the historical evolution of the work of Pedro Ortiz Cabanillas and his sociobiological informational theory]. / Apuntes sobre la evolución histórica de la obra de Pedro Ortiz Cabanillas y su teoría sociobiológica informacional.

The Informational Sociobiological Theory proposes a radically-different definition of living systems and, therefore, is the only existing neurological theory that evades the mind-brain problem and explains the nature of human consciousness. It was developed by Pedro Ortiz Cabanillas between 1984 and 2011. In this document we are presenting a listing of his main works. We include, additionally, unpublished material of the years 1998, 1999, 2006, and 2009.

La Teoría Sociobiológica Informacional propone una definición radicalmente distinta de los sistemas vivos, y con lo mismo es la única teoría neurológica existente que evade el problema mente-cerebro y que explica la naturaleza de la conciencia humana. Fue desarrollada por Pedro Ortiz Cabanillas entre 1984 y 2011. En este documento vamos a realizar un recuento de todas sus obras más importantes. Incluimos, adicionalmente, material inédito de los años 1998, 1999, 2006, y 2009.

Infoxicación en salud. La sobrecarga de información sobre salud en la web y el riesgo de que lo importante se haga invisible

Objetivo. Este estudio tiene como objetivos 1) crear conciencia del volumen de información en salud existente en la web de calidad, 2) explorar la percepción de profesionales de la información con relación al uso de fuentes cualificadas en la toma de decisiones en salud, y 3) presentar recomendaciones que permitan fortalecer las capacidades de los trabajadores de la salud y las competencias institucionales relacionadas con la alfabetización digital. Métodos. Se realizó un estudio no experimental descriptivo transversal con una muestra no probabilística de 32 profesionales de la información de nueve países. Se recopiló información de internet sobre el volumen de contenidos existentes en herramientas web, redes sociales y fuentes de información en salud. Se realizaron búsquedas en inglés y en español utilizando las palabras clave Ebola, Zika, Dengue, Chikungunya, Safe food, Health equity, Safe sex, y Obesit. Por último, se obtuvo información sobre la oferta de formación formal en temas de alfabetización digital, gestión de información y otros relacionados. Resultados. Seleccionando sólo cuatro enfermedades de alto impacto en salud pública en mayo de 2016 y promediando un tiempo de revisión mínimo de cada producto de información, se tardaría más de 50 años seguidos sin dormir para consultar todo lo publicado en línea sobre Dengue, Zika, Ebola y Chikungunja. Conclusión. Se concluye que la salud pública se beneficiaría con instituciones de salud que implementaran estrategias formales de gestión del conocimiento, con instituciones académicas de ciencias de la salud que incorporaran programas formales de alfabetización digital y con trabajadores de la salud cuyo desarrollo profesional sea responsable y funcional en la sociedad de la información.

Objective. The objectives of this study were to: 1) raise awareness of the volume of quality health information on the Internet; 2) explore perceptions of information professionals with regard to the use of qualified sources for health decision-making; and 3) make recommendations that facilitate strengthening health worker capacities and institutional competencies related to digital literacy. Methods. A non-experimental, descriptive cross-sectional study was conducted with a non-probability sample of 32 information professionals from nine countries. Internet information was compiled on the volume of content in Internet tools, social networks, and health information sources. Searches in English and Spanish were carried out using the keywords Ebola, Zika, dengue, chikungunya, safe food, health equity, safe sex, and obesity. Finally, information was obtained on opportunities for formal education on the subjects of digital literacy, information management, and other related topics. Results. Selecting only four diseases with a high impact on public health in May 2016 and averaging minimum review time for each information product, it would take more than 50 years without sleeping to consult everything that is published online about dengue, Zika, Ebola, and chikungunya. Conclusion. We conclude that public health would benefit from: health institutions implementing formal knowledge management strategies; academic health sciences institutions incorporating formal digital literacy programs; and having health workers who are professionally responsible and functional in the information society.

Objetivos. 1) Conscientizar sobre o volume de informação em saúde de qualidade existente na internet, 2) explorar a percepção dos profissionais da informação sobre o uso de fontes qualificadas na tomada de decisão em saúde e 3) fazer recomendações para reforçar o preparo dos profissionais de saúde e as competências institucionais quanto à alfabetização digital. Métodos. Foi realizado estudo transversal descritivo não experimental em uma amostra não probabilística com 32 profissionais da informação de nove países. Foi coletada informação da internet sobre o volume de conteúdos existentes sobre ferramentas de internet, redes sociais e fontes de informação em saúde. Foram realizadas buscas em inglês e espanhol utilizando as palavras-chave Ebola, Zika, Dengue, Chikungunya, Safe food, Health equity, Safe sex, e Obesity. E foi obtida informação sobre a oferta de cursos de formação em alfabetização digital, gestão da informação e outros tópicos relacionados. Resultados. Com a seleção de apenas quatro doenças de alto impacto em saúde pública em maio de 2016, com tempo de revisão médio mínimo para cada produto de informação, seriam necessários mais de 50 anos contínuos, sem intervalo para dormir, para consultar todo o conteúdo publicado online sobre dengue, zika, Ebola e chikungunya. Conclusão. Conclui-se que existiria benefício para a saúde pública se as instituições de saúde implementassem estratégias formais de gestão do conhecimento, as instituições acadêmicas de ciências da saúde incorporassem programas formais de alfabetização digital e os profissionais de saúde investissem em desenvolvimento profissional responsável e prático na sociedade da informação.

Validity of the Reading the Mind in the Eyes Test in a Brazilian Sample / Validez de la Reading the Mind in the Eyes Test en una Muestra Brasileña / Validade do Reading the Mind in the Eyes Test em uma Amostra Brasileira

Abstract: The Reading the Mind in the Eyes Test (RMET) is internationally used to assess emotional perception, but there are few validity studies with Brazilian samples. The test was answered by 1440 participants, along with the Computerized Test of Primary Emotions Perception (PEP), and abstract (AR) and verbal reasoning (VR) tasks. RMET items were studied with Rasch model. Results indicate that its items are concentrated at a lower level of difficulty, lacking difficult items to assess higher levels of emotional perception. Both RMET and PEP showed significant correlations with AR and VR, corroborating other studies showing emotional perception is related to other types of intelligence. However the correlation between RMET and PEP was lower than expected (r = .43), suggesting perception of emotions in the eyes is only partially related to perception in the whole face.

Resumo: O Reading the Mind in the Eyes Test (RMET) é utilizado internacionalmente para avaliação da percepção emocional, mas são poucos os estudosde validade com amostras brasileiras. O teste foi respondido por 1440 participantes, juntamente com o Teste Informatizado de Percepção de Emoções Primárias (PEP) e provas de raciocínio abstrato (RA) e verbal (RV). Os itens do RMET foram estudados com modelo de Rasch. Os resultados indicaram que os itens estão concentrados em um nível menor de dificuldade, com falta de itens difíceis para avaliar níveis mais altos de percepção emocional. Tanto o RMET quanto o PEP mostraram correlações significativas com RA e RV, corroborando estudos que mostram que percepção emocional está relacionada a outros tipos de inteligência. Contudo a correlação entre RMET e PEP foi menor do que esperada (r=0,43), sugerindo que percepção de emoção nos olhos está apenas parcialmente relacionada a percepção na face inteira.

Resumen: La Reading the Mind in theEyes Test (RMET) se utiliza internacionalmente para evaluar la percepción emocional, pero son pocos los estudios de validez con muestras brasileñas. La prueba fue respondida por 1440 participantes, junto con la Prueba Computarizada de Percepción de Emociones Primarias (PEP), y tareas de razonamiento abstracto (RA) y verbal (RV). Los ítems de la RMET fueron estudiados con el modelo de Rasch. Los resultados indicaron que sus elementos se concentran en un nivel inferior de dificultad, corto de ítems difíciles de evaluar niveles superiores de percepción emocional. Tanto RMET como PEP mostraron correlaciones significativas con RA y RV, corroborando otros estudios que muestran que la percepción emocional está relacionada con otros tipos de inteligencia. Sin embargo, la correlación entre RMET y PEP fue menor que lo esperado (r = 0,43), lo que sugiere que percepción de emociones en los ojos está sólo parcialmente relacionada con percepción en toda la cara.

Superlinear Summation of Information in Premotor Neuron Pairs.

Whether premotor/motor neurons encode information in terms of spiking frequency or by their relative time of firing, which may display synchronization, is still undetermined. To address this issue, we used an information theory approach to analyze neuronal responses recorded in the premotor (area F5) and primary motor (area F1) cortices of macaque monkeys under four different conditions of visual feedback during hand grasping. To evaluate the sensitivity of spike timing correlation between single neurons, we investigated the stimulus dependent synchronization in our population of pairs. We first investigated the degree of correlation of trial-to-trial fluctuations in response strength between neighboring neurons for each condition, and second estimated the stimulus dependent synchronization by means of an information theoretical approach. We compared the information conveyed by pairs of simultaneously recorded neurons with the sum of information provided by the respective individual cells. The information transmission across pairs of cells in the primary motor cortex seems largely independent, whereas information transmission across pairs of premotor neurons is summed superlinearly. The brain could take advantage of both the accuracy provided by the independency of F1 and the synergy allowed by the superlinear information population coding in F5, distinguishing thus the generalizing role of F5.

Information propagation in a noisy gene cascade.

We use information theory to study the information transmission through a simple gene cascade where the product of an unregulated gene regulates the expression activity of a cooperative genetic switch. While the input signal is provided by the upstream gene with two states, we consider that the expression of downstream gene is controlled by a cis-regulatory system with three binding sites for the regulator product, which can bind cooperatively. By computing exactly the associated probability distributions, we estimate information transmission thought the mutual information measure. We found that the mutual information associated with unimodal input signal is lower than the associated with bimodal inputs. We also observe that mutual information presents a maximum in the cooperativity intensity, and the position of this maximum depends on the kinetic rates of the promoter. Furthermore, we found that the bursting dynamics of the input signal can enhance the information transmission capacity.

Classification and Verification of Handwritten Signatures with Time Causal Information Theory Quantifiers.

We present a new approach for handwritten signature classification and verification based on descriptors stemming from time causal information theory. The proposal uses the Shannon entropy, the statistical complexity, and the Fisher information evaluated over the Bandt and Pompe symbolization of the horizontal and vertical coordinates of signatures. These six features are easy and fast to compute, and they are the input to an One-Class Support Vector Machine classifier. The results are better than state-of-the-art online techniques that employ higher-dimensional feature spaces which often require specialized software and hardware. We assess the consistency of our proposal with respect to the size of the training sample, and we also use it to classify the signatures into meaningful groups.