Decoding semiotic minimal genome: a non-genocentric approach.

The search for the minimum information required for an organism to sustain a cellular system network has rendered both the identification of a fixed number of known genes and those genes whose function remains to be identified. The approaches used in such search generally focus their analysis on coding genomic regions, based on the genome to proteic-product perspective. Such approaches leave other fundamental processes aside, mainly those that include higher-level information management. To cope with this limitation, a non-genocentric approach based on genomic sequence analysis using language processing tools and gene ontology may prove an effective strategy for the identification of those fundamental genomic elements for life autonomy. Additionally, this approach will provide us with an integrative analysis of the information value present in all genomic elements, regardless of their coding status.

The calculus of codes - From entropy, complexity, and information to life.

Exploring the core components that define living systems and their operational mechanisms within emerging biological entities is a complex endeavor. In the realm of biological systems literature, the terms matter, energy, information, complexity, and entropy are frequently referenced. However, possessing these concepts alone does not guarantee a comprehensive understanding or the ability to reconstruct the intricate nature of life. This study aims to illuminate the trajectory of these organic attributes, presenting a theoretical framework that delves into the integrated role of these concepts in biology. We assert that Code Biology serves as a pivotal steppingstone for unraveling the mechanisms underlying life. Biological codes (BCs) emerge not only from the interplay of matter and energy but also from Information. Contrary to deriving information from the former elements, we propose that information holds its place as a fundamental physical aspect. Consequently, we propose a continuum perspective called Calculus of Fundamentals involving three fundamentals: Matter, Energy, and Information, to depict the dynamics of BCs. To achieve this, we emphasize the necessity of studying Entropy and Complexity as integral organic descriptors. This perspective also facilitates the introduction of a mathematical theoretical framework that aids in comprehending continuous changes, the driving dynamics of biological fundamentals. We posit that Energy, Matter, and Information constitute the essential building blocks of living systems, and their interactions are governed by Entropy and Complexity analyses, redefined as biological descriptors. This interdisciplinary perspective of Code Biology sheds light on the intricate interplay between the controversial phenomenon of life and advances the idea of constructing a theory rooted in information as an organic fundamental.

Quantitative EEG analysis in typical absence seizures: unveiling spectral dynamics and entropy patterns.

A typical absence seizure is a generalized epileptic event characterized by a sudden, brief alteration of consciousness that serves as a hallmark for various generalized epilepsy syndromes. Distinguishing between similar interictal and ictal electroencephalographic (EEG) epileptiform patterns poses a challenge. However, quantitative EEG, particularly spectral analysis focused on EEG rhythms, shows potential for differentiation. This study was designed to investigate discernible differences in EEG spectral dynamics and entropy patterns during the pre-ictal and post-ictal periods compared to the interictal state. We analyzed 20 EEG ictal patterns from 11 patients with confirmed typical absence seizures, and assessed recordings made during the pre-ictal, post-ictal, and interictal intervals. Power spectral density (PSD) was used for the quantitative analysis that focused on the delta, theta, alpha, and beta bands. In addition, we measured EEG signal regularity using approximate (ApEn) and multi-scale sample entropy (MSE). Findings demonstrate a significant increase in delta and theta power in the pre-ictal and post-ictal intervals compared to the interictal interval, especially in the posterior brain region. We also observed a notable decrease in entropy in the pre-ictal and post-ictal intervals, with a more pronounced effect in anterior brain regions. These results provide valuable information that can potentially aid in differentiating epileptiform patterns in typical absence seizures. The implications of our findings are promising for precision medicine approaches to epilepsy diagnoses and patient management. In conclusion, our quantitative analysis of EEG data suggests that PSD and entropy measures hold promise as potential biomarkers for distinguishing ictal from interictal epileptiform patterns in patients with confirmed or suspected typical absence seizures.

Unraveling the hCoV-19 Informational Architecture.

The hCoV-19 virus is continuously evolving to highly infectious and lethal variants. There is a latent risk that current vaccines will not be effective over these novel variants. This entails comprehending the genome-wide viral information to unveil mutagenic mechanisms of hCoV-19. To date, this virus is studied as a collection of non-related variants, making it challenging to forecast hotspots and their upcoming effects. In this work, we explore genome-wide information to disentangle informational mechanisms that lead to insights into viral mutagenicity. Towards this aim, we modeled informational compartments based on a topic-free-alignment workflow. These compartments illustrate that hCoV-19 has a complex informational architecture that addresses high-level virus phenomena, i.e., mutagenicity. This new framework represents the first step towards identifying the virus mutagenicity leading to the development of all-variants-effective vaccines.

Multilayer Network Approach in EEG Motor Imagery with an Adaptive Threshold.

The brain has been understood as an interconnected neural network generally modeled as a graph to outline the functional topology and dynamics of brain processes. Classic graph modeling is based on single-layer models that constrain the traits conveyed to trace brain topologies. Multilayer modeling, in contrast, makes it possible to build whole-brain models by integrating features of various kinds. The aim of this work was to analyze EEG dynamics studies while gathering motor imagery data through single-layer and multilayer network modeling. The motor imagery database used consists of 18 EEG recordings of four motor imagery tasks: left hand, right hand, feet, and tongue. Brain connectivity was estimated by calculating the coherence adjacency matrices from each electrophysiological band (δ, θ, α and ß) from brain areas and then embedding them by considering each band as a single-layer graph and a layer of the multilayer brain models. Constructing a reliable multilayer network topology requires a threshold that distinguishes effective connections from spurious ones. For this reason, two thresholds were implemented, the classic fixed (average) one and Otsu's version. The latter is a new proposal for an adaptive threshold that offers reliable insight into brain topology and dynamics. Findings from the brain network models suggest that frontal and parietal brain regions are involved in motor imagery tasks.

A Transcriptome Community-and-Module Approach of the Human Mesoconnectome.

Graph analysis allows exploring transcriptome compartments such as communities and modules for brain mesostructures. In this work, we proposed a bottom-up model of a gene regulatory network to brain-wise connectome workflow. We estimated the gene communities across all brain regions from the Allen Brain Atlas transcriptome database. We selected the communities method to yield the highest number of functional mesostructures in the network hierarchy organization, which allowed us to identify specific brain cell functions (e.g., neuroplasticity, axonogenesis and dendritogenesis communities). With these communities, we built brain-wise region modules that represent the connectome. Our findings match with previously described anatomical and functional brain circuits, such the default mode network and the default visual network, supporting the notion that the brain dynamics that carry out low- and higher-order functions originate from the modular composition of a GRN complex network.

Metacode: One code to rule them all.

The code of codes or metacode is a microcosm where biological layers, as well as their codes, interact together allowing the continuity of information flow in organisms by increasing biological entities' complexity. Through this novel organic code, biological systems scale towards niches with higher informatic freedom building structures that increase the entropy in the universe. Code biology has developed a novel informational framework where biological entities strive themselves through the information flow carried out through organic codes consisting of two molecular or functional landscapes intertwined through arbitrary linkages via an adaptor whose nature is autonomous from molecular determinism. Here we will integrate genomic and epigenomic codes according to the evidence released in ENCODE (phase 3), psychENCODE and GTEx project, outlining the principles of the metacode, to address the continuous nature of biological systems and their inter-layered information flow. This novel complex metacode maps from very constrained sets of elements (i.e., regulation sites modulating gene expression) to new ones with greater freedom of decoding (i.e., a continuous cell phenotypic space). This leads to a new domain in code biology where biological systems are informatic attractors that navigate an energy metaspace through a complexity-noise balance, stalling in emergent niches where organic codes take meaning.

Whole-Genome k-mer Topic Modeling AssociatesBacterial Families.

Alignment-free k-mer-based algorithms in whole genome sequence comparisons remainan ongoing challenge. Here, we explore the possibility to use Topic Modeling for organismwhole-genome comparisons. We analyzed 30 complete genomes from three bacterial families bytopic modeling. For this, each genome was considered as a document and 13-mer nucleotiderepresentations as words. Latent Dirichlet allocation was used as the probabilistic modeling of thecorpus. We where able to identify the topic distribution among analyzed genomes, which is highlyconsistent with traditional hierarchical classification. It is possible that topic modeling may be appliedto establish relationships between genome's composition and biological phenomena.

A code biology analysis of the regulatory regions in cell lines / Análisis de biología de códigos de las regiones reguladoras en líneas celulares

Abstract Coding sequences are widely studied for their relevance in protein synthesis. However, higher organism genomes, such as human genomes, has a small amount of them, and a larger proportion of non-coding sequences. ENCODE and Epigenomic Roadmap projects discovered that regulatory functions are carried out in the non-coding regions of the human genome. These regulatory functions are part of the regulatory machinery that yields different gene expression profiles, thus, different cell lines. Whereas different environmental elements, i. e. histone modifications, DNA methylation, and other epigenomic phenomena, determine the regulatory function of genome part, the sequences' composition where these functions take place could also influence regulatory machinery. In this work, we explore the non-coding regulatory sequences and lexica build with subsequences between 3 and 16 nucleotides to evaluate the difference between the sequence composition of the regulatory regions in the cell lines. Our results show that the lexica corresponding to the regulatory regions are different based on their complexity/degeneracy, moreover, the lexica of regulatory regions in different cell lines are also different. These features suggest that non-coding sequences are an active element of the regulatory machinery and the histone code that are involved in cell differentiation.

Resumen Las secuencias codificantes han sido ampliamente estudiadas por su relevancia en la síntesis de proteínas. Sin embargo, los genomas de organismos complejos, como el humano, tiene una porción menor de estas secuencias y una mayor proporción de secuencias no codificantes. Los proyectos del ENCODE y Epigenomic Roadmap describieron que las funciones reguladoras se llevan acabo en las regiones no codificantes del genoma humano. Estas funciones reguladoras son parte de la maquinaria reguladora que produce diferentes perfiles de expresión genética, por tanto, diferentes líneas celulares. Mientras diferentes elementos del entorno, como las modificaciones en las histonas, metilación del ADN y otros fenómenos epigenéticos, determinan la función reguladora que tienen una porción del genoma, la composición de la secuencia donde estas funciones son llevadas a cabo también podrían influir en la maquinaria reguladora. En este trabajo, se exploraron las secuencias de las regiones no codificantes y los léxicos generados con las subsecuencias entre 3 y 16 nucleótidos, para evaluar las diferencias entre la composición de las secuencias de las regiones reguladoras en las líneas celulares. Los resultados muestran que los léxicos correspondientes a las regiones reguladoras son diferentes con base en su complejidad/degeneración, así mismo, los léxicos de las regiones reguladoras en distintas líneas celulares son también distintos. Estos detalles sugieren que las secuencias no codificantes son elemento activo de la maquinaria reguladora y del código histónico que participan en la diferenciación celular.

Water availability not fruitfall modulates the dry season distribution of frugivorous terrestrial vertebrates in a lowland Amazon forest.

Terrestrial vertebrate frugivores constitute one of the major guilds in tropical forests. Previous studies show that the meso-scale distribution of this group is only weakly explained by variables such as altitude and tree basal area in lowland Amazon forests. For the first time we test whether seasonally limiting resources (water and fallen fruit) affect the dry season distribution in 25 species of terrestrial vertebrates. To examine the effects of the spatial availability of fruit and water on terrestrial vertebrates we used a standardized, regularly spaced arrangement of camera-traps within 25km2 of lowland Amazon forest. Generalized linear models (GLMs) were then used to examine the influence of four variables (altitude, distance to large rivers, distance to nearest water, and presence vs absence of fruits) on the number of photos on five functional groups (all frugivores, small, medium, large and very large frugivores) and on seven of the most abundant frugivore species (Cuniculus paca, Dasyprocta leporina, Mazama americana, Mazama nemorivaga, Myoprocta acouchy, Pecari tajacu and Psophia crepitans). A total of 279 independent photos of 25 species were obtained from 900 camera-trap days. For most species and three functional groups, the variation in the number of photos per camera was significantly but weakly explained by the GLMs (deviance explained ranging from 6.2 to 48.8%). Generally, we found that the presence of water availability was more important than the presence of fallen fruit for the groups and species studied. Medium frugivores, large-bodied frugivores, and two of the more abundant species (C. paca and P. crepitans) were recorded more frequently closer to water bodies; while none of the functional groups nor the most abundant species showed any significant relationship with the presence of fallen fruit. Two functional groups and two of the seven most common frugivore species assessed in the GLMs showed significant results with species-specific responses to altitude. Our findings provide a more detailed understanding of how frugivorous vertebrates cope with periods of water and fruit scarcity in lowland Amazon forests.

[Gastric cancer in a general hospital. Santa Rosa Hospital. Experience]. / Cáncer gástrico en un hospital general: Hospital Santa Rosa.

PURPOSE: Determine the frequency of gastric cancer and its clinical and pathological characteristics, clinical stages, surgical treatment, morbimortality and survival in a general hospital. MATERIALS AND METHODS: Retrospective, descriptive study on 71 consecutive patients diagnosed with gastric cancer at the Santa Rosa Hospital from January 1, 2005 to January 31, 2008. RESULTS: During the study period, 71 cases of gastric adenocarcinoma were confirmed by histopathology. This disease is more frequent in men, with a 1.54 to 1 ratio, as compared to women. The most frequent age of appearance is between the fifth and seventh decades of life. Distal tumors (81.7%) are four times more common than proximal tumors (18,3%). The most common histological type was carcinoma in signet-ring cells (40.8%). The most frequent degree of differentiation was Undifferentiated (42.3%). A 62% (n=44) of patients entered the operating room. The resectability rate was 68% (n=30). The advanced stage was the most common form of presentation in patients (97.2%), while the early stage was rare (2.8%). The most frequent surgeries were the distal subtotal gastrectomy (73.3%) and the total gastrectomy (26.7%). The D2 (73.3%) dissection was performed. The mortality rate was 6.7% and the morbidity rate was 26.7%. Survival was better in patients who underwent resection than in patients who only underwent biopsy or were unresectable, evidencing statistical significance. CONCLUSION: Gastric cancer is diagnosed in a late stage and surgical treatment plays a pivotal role and, even in advanced cases, morbidity/mortality is acceptable for the initial experience at a third-level general hospital. It is necessary to carry out screening program to detect the disease in earlier stages.

Cáncer Gástrico en un Hospital General: Hospital Santa Rosa / Gastric cancer in a general hospital. Santa Rosa Hospital. experience

OBJETIVO: Determinar la frecuencia de cáncer gástrico y sus características clínico patológicas, estadios clínicos, tratamiento quirúrgico, morbimortalidad y sobrevida en un hospital general. MATERIALES Y MÉTODOS: Estudio retrospectivo, descriptivo, de 71 pacientes consecutivos diagnosticados con cáncer gástrico en el Hospital Santa Rosa desde el 1 de enero 2005 hasta el 31 de enero 2008. RESULTADOS: En el periodo de estudio se confirmaron por histopatologia 71 casos de adenocarcinoma gástrico. El sexo masculino es el más frecuente, con una relación de 1,54 a 1 con respecto al sexo femenino. La edad de presentación más frecuente se encuentra entre la 5ta y 7ma década de vida. Los tumores distales (81,7 por ciento) son cuatro veces más frecuentes que los proximales (18,3 por ciento). El tipo histológico más frecuente fue el carcinoma en células de anillo de sello (40,8 por ciento). El grado de diferenciación más frecuente fue el Indiferenciado (42,3 por ciento). El 62 por ciento (n=44) ingresó a sala de operaciones. La tasa de resecabilidad fue de 68 por ciento (n=30). El estadío clínico avanzado ha sido la forma depresentación más frecuente de los pacientes (97,2 por ciento), mientras que el estadío precoz ha sido raro (2,8 por ciento). La cirugía más frecuente fue la gastrectomía subtotal distal (73,3 por ciento) y gastrectomía total (26,7 por ciento). La disección realizada fue la D2 (73,3 por ciento). La tasa de mortalidadfue 6,7 por ciento y morbilidad de 26,7 por ciento. La sobrevida fue mejor en los pacientes que tuvieron resección frente a los que sólo se les realizó biopsia o fueron irresecables, evidenciandosignificancia estadística. CONCLUSIÓN: El cáncer gástrico se diagnóstica en etapa tardía y el tratamiento quirúrgicojuega un rol fundamental e incluso en casos avanzados, la morbimortalidad es aceptable para la experiencia inicial en un Hospital general de tercer nivel. Es necesario realizar programas de tamizaje para detectar la enfermedad en...

PURPOSE: Determine the frequency of gastric cancer and its clinical and pathological characteristics, clinical stages, surgical treatment, morbimortality and survival in ageneral hospital. MATERIALS AND METHODS: Retrospective, descriptive study on 71 consecutive patients diagnosed with gastric cancer at the Santa Rosa Hospital from January 1, 2005 to January 31, 2008. RESULTS: During the study period, 71 cases of gastric adenocarcinoma were confirmed by histopathology. This disease is more frequent in men, with a 1.54 to 1 ratio, as compared to women. The most frequent age of appearance is between the fifth and seventh decadesof life. Distal tumors (81.7 per cent) are four times more common than proximal tumors (18,3 per cent).The most common histological type was carcinoma in signet-ring cells (40.8 per cent). The mostfrequent degree of differentiation was Undifferentiated (42.3 per cent). A 62 per cent (n=44) of patients entered the operating room. The resectability rate was 68 per cent (n=30). The advanced stagewas the most common form of presentation in patients (97.2 per cent), while the early stage was rare (2.8 per cent). The most frequent surgeries were the distal subtotal gastrectomy (73.3 per cent) and the total gastrectomy (26.7 per cent). The D2 (73.3 per cent) dissection was performed. The mortality rate was 6.7 per cent and the morbidity rate was 26.7 per cent. Survival was better in patients who underwent resection than in patients who only underwent biopsy or were unresectable, evidencing statistical significance. CONCLUSIÓN: Gastric cancer is diagnosed in a late stage and surgical treatment playsa pivotal role and, even in advanced cases, morbidity/mortality is acceptable for the initial experience at a third-level general hospital. It is necessary to carry out screening program to detect the disease in earlier stages.

Banco de huesos: Obtención, conservación y utilización de injertos oseos esponjos de banco / Bank of bones: Obtaining, conservation and use of esponjos bony grafts of bank

Constituye una guía médica para la atención de pacientes con lesiones oseas. Presenta la organización y metodología de los bancos de huesos, así como las normas para el uso y conservación del material oseo esponjoso...