Rule-Based Models and Applications in Biology.

Complex systems are governed by dynamic processes whose underlying causal rules are difficult to unravel. However, chemical reactions, molecular interactions, and many other complex systems can be usually represented as concentrations or quantities that vary over time, which provides a framework to study these dynamic relationships. An increasing number of tools use these quantifications to simulate dynamically complex systems to better understand their underlying processes. The application of such methods covers several research areas from biology and chemistry to ecology and even social sciences.In the following chapter, we introduce the concept of rule-based simulations based on the Stochastic Simulation Algorithm (SSA) as well as other mathematical methods such as Ordinary Differential Equations (ODE) models to describe agent-based systems. Besides, we describe the mathematical framework behind Kappa (κ), a rule-based language for the modeling of complex systems, and some extensions for spaßtial models implemented in PISKaS (Parallel Implementation of a Spatial Kappa Simulator). To facilitate the understanding of these methods, we include examples of how these models can be used to describe population dynamics in a simple predator-prey ecosystem or to simulate circadian rhythm changes.

Guaranteed Outlier Removal for Point Cloud Registration with Correspondences.

An established approach for 3D point cloud registration is to estimate the registration function from 3D keypoint correspondences. Typically, a robust technique is required to conduct the estimation, since there are false correspondences or outliers. Current 3D keypoint techniques are much less accurate than their 2D counterparts, thus they tend to produce extremely high outlier rates. A large number of putative correspondences must thus be extracted to ensure that sufficient good correspondences are available. Both factors (high outlier rates, large data sizes) however cause existing robust techniques to require very high computational cost. In this paper, we present a novel preprocessing method called guaranteed outlier removal for point cloud registration. Our method reduces the input to a smaller set, in a way that any rejected correspondence is guaranteed to not exist in the globally optimal solution. The reduction is performed using purely geometric operations which are deterministic and fast. Our method significantly reduces the population of outliers, such that further optimization can be performed quickly. Further, since only true outliers are removed, the globally optimal solution is preserved. On various synthetic and real data experiments, we demonstrate the effectiveness of our preprocessing method. Demo code is available as supplementary material, which can be found on the Computer Society Digital Library at http://doi.ieeecomputersociety.org/10.1109/TPAMI.2017.2773482.

Stochastic simulation of multiscale complex systems with PISKaS: A rule-based approach.

Computational simulation is a widely employed methodology to study the dynamic behavior of complex systems. Although common approaches are based either on ordinary differential equations or stochastic differential equations, these techniques make several assumptions which, when it comes to biological processes, could often lead to unrealistic models. Among others, model approaches based on differential equations entangle kinetics and causality, failing when complexity increases, separating knowledge from models, and assuming that the average behavior of the population encompasses any individual deviation. To overcome these limitations, simulations based on the Stochastic Simulation Algorithm (SSA) appear as a suitable approach to model complex biological systems. In this work, we review three different models executed in PISKaS: a rule-based framework to produce multiscale stochastic simulations of complex systems. These models span multiple time and spatial scales ranging from gene regulation up to Game Theory. In the first example, we describe a model of the core regulatory network of gene expression in Escherichia coli highlighting the continuous model improvement capacities of PISKaS. The second example describes a hypothetical outbreak of the Ebola virus occurring in a compartmentalized environment resembling cities and highways. Finally, in the last example, we illustrate a stochastic model for the prisoner's dilemma; a common approach from social sciences describing complex interactions involving trust within human populations. As whole, these models demonstrate the capabilities of PISKaS providing fertile scenarios where to explore the dynamics of complex systems.

Cirugía laparoscópica de una hernia de Garengeot: presentación poco frecuente de una hernia crural / Laparoscopic Surgery of a Garengeot's Hernia: A rare presentation of a crural hernia

Introducción: La hernia de Garengeot es una rara presentación de una hernia crural. Caso clínico: Se presenta el caso de una mujer de 64 años de edad, que consultó por dolor en fosa ilíaca derecha. Se le realizó una tomografía axial, que mostró un proceso inflamatorio en cuadrante inferior derecho del abdomen. Se le practicó una laparoscopia exploradora, encontrando el apéndice cecal en el anillo crural. Se realizó apendicectomía y reparación de la hernia vía laparoscópica. En nuestra revisión este es el tercer caso publicado en el mundo de resolución laparoscópica, y el primero en Chile.

Background: Garengeot's hernia is a rare presentation of a femoral hernia. Case report: We report a case of a 64 year-old female patient complaining of right lower abdominal pain. She was studied by CT-Scan that showed an inflammatory process in right lower cuadrant. We made an exploratory laparoscopy and found the cecal appendix in the crural defect. We did a laparoscopic appendectomy and crural hernia repair with mesh. To our knowledge, this is the third laparoscopic case published in the world and the first of Chile.

Fast Rotation Search with Stereographic Projections for 3D Registration.

Registering two 3D point clouds involves estimating the rigid transform that brings the two point clouds into alignment. Recently there has been a surge of interest in using branch-and-bound (BnB) optimisation for point cloud registration. While BnB guarantees globally optimal solutions, it is usually too slow to be practical. A fundamental source of difficulty lies in the search for the rotational parameters. In this work, first by assuming that the translation is known, we focus on constructing a fast rotation search algorithm. With respect to an inherently robust geometric matching criterion, we propose a novel bounding function for BnB that is provably tighter than previously proposed bounds. Further, we also propose a fast algorithm to evaluate our bounding function. Our idea is based on using stereographic projections to precompute and index all possible point matches in spatial R-trees for rapid evaluations. The result is a fast and globally optimal rotation search algorithm. To conduct full 3D registration, we co-optimise the translation by embedding our rotation search kernel in a nested BnB algorithm. Since the inner rotation search is very efficient, the overall 6DOF optimisation is speeded up significantly without losing global optimality. On various challenging point clouds, including those taken out of lab settings, our approach demonstrates superior efficiency.

Predetermined embryonic glial cells form the distinct glial sheaths of the Drosophila peripheral nervous system.

One of the numerous functions of glial cells in Drosophila is the ensheathment of neurons to isolate them from the potassium-rich haemolymph, thereby establishing the blood-brain barrier. Peripheral nerves of flies are surrounded by three distinct glial cell types. Although all embryonic peripheral glia (ePG) have been identified on a single-cell level, their contribution to the three glial sheaths is not known. We used the Flybow system to label and identify each individual ePG in the living embryo and followed them into third instar larva. We demonstrate that all ePG persist until the end of larval development and some even to adulthood. We uncover the origin of all three glial sheaths and describe the larval differentiation of each peripheral glial cell in detail. Interestingly, just one ePG (ePG2) exhibits mitotic activity during larval stages, giving rise to up to 30 glial cells along a single peripheral nerve tract forming the outermost perineurial layer. The unique mitotic ability of ePG2 and the layer affiliation of additional cells were confirmed by in vivo ablation experiments and layer-specific block of cell cycle progression. The number of cells generated by this glial progenitor and hence the control of perineurial hyperplasia correlate with the length of the abdominal nerves. By contrast, the wrapping and subperineurial glia layers show enormous hypertrophy in response to larval growth. This characterisation of the embryonic origin and development of each glial sheath will facilitate functional studies, as they can now be addressed distinctively and genetically manipulated in the embryo.

[Acute meningitis in Córdoba, Colombia (2002-2004)]. / Meningitis agudas en Córdoba, Colombia 2002-2004.

OBJECTIVE: Establishing characteristic epidemiologic and microbiologic features of acute meningitis in the Córdoba department. METHODOLOGY: A descriptive epidemiological study was carried out between June 2002 and June 2004 at the Hospital San Jerónimo in Montería. All suspicious cases of meningitis were included; laboratory tests included cytological smear, biochemistry, latex, Gram stain and culture. RESULTS: 57 (11.3%) and 85 (16.8%) of the 503 samples of cerebrum spinal fluid (CSF) were confirmed by culture as being probable cases. There were 6 cases of polymicrobial infection, making a total of 63 isolates: 17 non-fermenting Gram-negative bacilli (26.9%), 16 Streptococcus pneumoniae (25.4%), 7 Enterobacteriaceae (11%), 5 Criptococcus neoformans (8%) 4 Neisseria meningitidis serotype B (6.3%), 3 S. viridans (4.8%), 2 Streptococcus group B (3.2%), 2 Haemophilus influenzae type B (3.2%), 2 Staphylococcus negative coagulase (3.2%), 2 S. aureus (3.2%), 2 Enterococcus (3.2%) and 1 Candida albicans (1.6%). The S. Pneumoniae serotypes found were: 5 (n=4), 23F (n=3), 14 (n=2), 18C (n=2), 18A (n=l1, 17F (n=l1, 1 (n=1). CONCLUSIONS: The study led to determining epidemiological and microbiological aspects of acute meningitis in the Códoba department which had been unknown up to now. Streptococcus pneumoniae (25.4% was the main aetiological agent of meningitis; the epidemiologic aspects so established confirmed the need for strengthening and implementing measures for controlling meningitis in C6ódoba and its surveillance there.

Meningitis Agudas en Córdoba, Colombia 2002 - 2004 / Acute meningitis in Córdoba, Colombia (2002-2004)

Objetivo: Establecer las características epidemiológicas y microbiológicas de las meningitis agudas del departamento de Córdoba. Métodos: Se realizó un estudio descriptivo de vigilancia epidemiológica en el Hospital San Jerónimo de Montería. Se tomaron todos los casos de meningitis, presentados (junio 2002 - junio 2004), las pruebas de laboratorio incluyeron: citoquímico, prueba de látex, tinción de Gram y cultivo. Resultados: Se analizaron 503 muestras de liquido cefalorraquídeo, confirmados por cultivo 57 (11,3 por ciento) casos y 85 (16,8 por ciento) casos probables. Se presentaron 63 aislamientos distribuidos así: 17 bacilos Gram negativos no fermentadores (26,9 por ciento), 16 Streptococcus pneumoniae (25,4 por ciento), 7 Enterobacterias (1 por ciento), 5 Criptococcus neoformans (8 por ciento), 4 Neisseria meningitidis serotipo B (6,3 por ciento), 3 S. viridans (4,8 por ciento), 2 Streptococcus grupo B (3,2 por ciento), 2 Haemophilus influenzae tipo B (3,2 por ciento), 2 S. aureus (3,2 por ciento), 2 Staphylococcus coagulasa negativos (3,2 por ciento), 2 Enterococcus (3,2 por ciento) y 1 Candida albicans (1,6 por ciento). Los serotipos de S. Pneumoniae fueron: 5 (n=4), 23F (n=3), 14 (n=2), 18C (n=2), 18A (n=1), 17F (n=1), 1 (n=1). Conclusión: El estudio permitió determinar los aspectos epidemiológicos y microbiológicos hasta ahora desconocidos de las meningitis agudas en el departamento de Córdoba. Streptococcus pneumoniae (25,4 por ciento) fue el principal agente causal de meningitis, los aspectos epidemiológicos establecidos confirman la necesidad de fortalecer e implantar medidas para el control y vigilancia de las meningitis en Córdoba.

Escepticemia: una condición deseable / Escepticemia: a desirable condition

En tono de ensayo, el autor advierte sobre los diversos riesgos que implica la publicación de artículos médicos y da ejemplos de cómo es posible que la investigación clínica se desvíe de sus objetivos si no se desarrolla bajo la lupa del escepticismo, una condición necesaria para evitar el error y aproximarse a la verdad, aunque ésta sea provisoria. El artículo critica el autoritarismo en medicina, la deshumanización médica y la aplicación sesgada de los principios de la medicina basada en la evidencia

El enfoque en el consultorio del niño con infección aguda / The foccussing in the child consultory with acute infections

No todo el manejo de los pacientes debe ser cuidados intensivos con equipo costoso y complicado. Hay que revaluar los criterios clínicos y volver a hacer sentir al médico su capacidad para visitar a sus enfermos en casa, especialmente en las ciudades pequeñas. Esta actitud tiene una gran importancia para la tranquilidad familiar pero, sobre todo, para el bienestar del niño enfermo