Flexible comparative genomics of prokaryotic transcriptional regulatory networks.

BACKGROUND: Comparative genomics methods enable the reconstruction of bacterial regulatory networks using available experimental data. In spite of their potential for accelerating research into the composition and evolution of bacterial regulons, few comparative genomics suites have been developed for the automated analysis of these regulatory systems. Available solutions typically rely on precomputed databases for operon and ortholog predictions, limiting the scope of analyses to processed complete genomes, and several key issues such as the transfer of experimental information or the integration of regulatory information in a probabilistic setting remain largely unaddressed. RESULTS: Here we introduce CGB, a flexible platform for comparative genomics of prokaryotic regulons. CGB has few external dependencies and enables fully customized analyses of newly available genome data. The platform automates the merging of experimental information and uses a gene-centered, Bayesian framework to generate and integrate easily interpretable results. We demonstrate its flexibility and power by analyzing the evolution of type III secretion system regulation in pathogenic Proteobacteria and by characterizing the SOS regulon of a new bacterial phylum, the Balneolaeota. CONCLUSIONS: Our results demonstrate the applicability of the CGB pipeline in multiple settings. CGB's ability to automatically integrate experimental information from multiple sources and use complete and draft genomic data, coupled with its non-reliance on precomputed databases and its easily interpretable display of gene-centered posterior probabilities of regulation provide users with an unprecedented level of flexibility in launching comparative genomics analyses of prokaryotic transcriptional regulatory networks. The analyses of type III secretion and SOS response regulatory networks illustrate instances of convergent and divergent evolution of these regulatory systems, showcasing the power of formal ancestral state reconstruction at inferring the evolutionary history of regulatory networks.

Ecocardiografía de estrés extrahospitalaria: necesidad de adecuar las unidades de imagen cardiaca a la guía europea de síndrome coronario crónico / Stress echocardiography in nonhospital centers: need to reorganize imaging units according to guidelines on chronic coronary syndromes

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The Super-Stückelberg procedure and dS in pure supergravity.

Understanding de Sitter space in supergravity-and string theory-has led to an intense amount of work for more than two decades, largely motivated by the discovery of the accelerated expansion of the Universe in 1998. In this paper, we consider a non-trivial generalization of unimodular gravity to minimal N = 1 supergravity, which allows for de Sitter solutions without the need of introducing any matter. We formulate a superspace version of the Stückelberg procedure, which restores diffeomorphism and local supersymmetry invariance. This introduces the goldstino associated with spontaneous breaking of supersymmetry in a natural way. The cosmological constant and gravitino mass are related to the vacuum expectation value of the components of a Lagrange multiplier imposing a super-unimodularity condition.

Dark Energy after GW170817 Revisited.

We revisit the status of scalar-tensor theories with applications to dark energy in the aftermath of the gravitational wave signal GW170817 and its optical counterpart GRB170817A. At the level of the cosmological background, we identify a class of theories, previously declared unviable in this context, whose anomalous gravitational wave speed is proportional to the scalar equation of motion. As long as the scalar field is assumed not to couple directly to matter, this raises the possibility of compatibility with the gravitational wave data, for any cosmological sources, thanks to the scalar dynamics. This newly "rescued" class of theories includes examples of generalized quintic Galileons from Horndeski theories. Despite the promise of this leading order result, we show that the loophole ultimately fails when we include the effect of large scale inhomogeneities.

A Systematic Review of Perception System and Simulators for Autonomous Vehicles Research.

This paper presents a systematic review of the perception systems and simulators for autonomous vehicles (AV). This work has been divided into three parts. In the first part, perception systems are categorized as environment perception systems and positioning estimation systems. The paper presents the physical fundamentals, principle functioning, and electromagnetic spectrum used to operate the most common sensors used in perception systems (ultrasonic, RADAR, LiDAR, cameras, IMU, GNSS, RTK, etc.). Furthermore, their strengths and weaknesses are shown, and the quantification of their features using spider charts will allow proper selection of different sensors depending on 11 features. In the second part, the main elements to be taken into account in the simulation of a perception system of an AV are presented. For this purpose, the paper describes simulators for model-based development, the main game engines that can be used for simulation, simulators from the robotics field, and lastly simulators used specifically for AV. Finally, the current state of regulations that are being applied in different countries around the world on issues concerning the implementation of autonomous vehicles is presented.

Endocarditis infecciosa en pacientes con enfermedades oncológicas / Infective endocarditis in patients with oncological diseases

Introducción: Los pacientes con cáncer pueden constituir un especial grupo de riesgo para el desarrollo de endocarditis infecciosa (EI) debido a que frecuentemente están sometidos a maniobras invasivas. Nuestro objetivo es conocer cuál es el perfil diferencial y el pronóstico de los pacientes con EI y cáncer. Métodos: Estudio observacional retrospectivo de todos los pacientes con EI diagnosticados consecutivamente en un hospital entre 2005 y 2015. Se realiza un análisis comparativo entre los pacientes con enfermedad oncológica y sin ella, así como un seguimiento a largo plazo. Resultados: Se diagnosticaron 208 casos de EI, de los cuales 32 sufrían enfermedad oncológica. No hubo diferencias significativas en cuanto a la edad (67,5 [59,2-74] vs. 64 [51-74] años), y la comorbilidad estimada por el índice de Charlson fue similar cuando no se consideró el propio diagnóstico de cáncer (4 [2,2-5] vs. 3,9 [2-5]). Se relacionó principalmente con la asistencia sanitaria (59,5% vs. 24,4%, p<0,001), predominó Staphylococcus aureus como agente causal (35%) y la localización tricuspídea fue 3 veces más frecuente (18,8% vs. 6,2%). Un 18,7% de pacientes no se intervinieron quirúrgicamente a pesar de tener indicación, frente al 7,4% de pacientes sin cáncer. La mortalidad intrahospitalaria alcanzó el 45,5% en pacientes con cáncer y la probabilidad de supervivencia al año fue del 40%. Conclusiones: La EI en pacientes con cáncer está predominantemente causada por estafilococos y presenta una elevada mortalidad precoz. A pesar de que se relaciona frecuentemente con la asistencia sanitaria, los pacientes se ven limitados desde el punto de vista terapéutico (AU)

Introduction: Cancer patients may constitute a special risk group for the development of infective endocarditis (IE) because they are often subjected to invasive procedures. The aim of this study is to determine the differential clinical profile and prognosis of patients with IE and cancer. Methods: A retrospective observational study was conducted on all patients consecutively diagnosed with IE in a single centre between 2005 and 2015. A comparative analysis was performed between patients with cancer and those free of disease, as well as a long-term follow-up. Results: There were 208 IE cases, of which 32 had a cancer diagnosis. There were no significant differences in age (67.5 [59.2-74] vs. 64 [51-74] years). The Charlson comorbidity index was same whether cancer was diagnosed or not (4 [2.2-5] vs. 3.9 [2-5]). IE in cancer patients was mainly associated with health care (59.5% vs 24.4%, P<.001). Staphylococcus aureus was the main causative agent (35%), and the tricuspid location was three times more common (18.8% vs. 6.2%). Surgery was not performed in 18.7% of patients, despite having an indication, compared with 7.4% of patients without cancer. In-hospital mortality for cancer patients was 45.5%, and the probability of survival at one year was 40%. Conclusions: IE in patients with cancer is predominantly caused by staphylococci, and has high early mortality. Although it is often related to health care, patients are limited from the therapeutic point of view (AU)

Infective endocarditis in patients with oncological diseases. / Endocarditis infecciosa en pacientes con enfermedades oncológicas.

INTRODUCTION: Cancer patients may constitute a special risk group for the development of infective endocarditis (IE) because they are often subjected to invasive procedures. The aim of this study is to determine the differential clinical profile and prognosis of patients with IE and cancer. METHODS: A retrospective observational study was conducted on all patients consecutively diagnosed with IE in a single centre between 2005 and 2015. A comparative analysis was performed between patients with cancer and those free of disease, as well as a long-term follow-up. RESULTS: There were 208 IE cases, of which 32 had a cancer diagnosis. There were no significant differences in age (67.5 [59.2-74] vs. 64 [51-74] years). The Charlson comorbidity index was same whether cancer was diagnosed or not (4 [2.2-5] vs. 3.9 [2-5]). IE in cancer patients was mainly associated with health care (59.5% vs 24.4%, P<.001). Staphylococcus aureus was the main causative agent (35%), and the tricuspid location was three times more common (18.8% vs. 6.2%). Surgery was not performed in 18.7% of patients, despite having an indication, compared with 7.4% of patients without cancer. In-hospital mortality for cancer patients was 45.5%, and the probability of survival at one year was 40%. CONCLUSIONS: IE in patients with cancer is predominantly caused by staphylococci, and has high early mortality. Although it is often related to health care, patients are limited from the therapeutic point of view.

Embolias sistémicas. La importancia de la ecocardiografía transesofágica / Systemic emboli: the importance of transesophageal echocardiography

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Surgical treatment of congenital torticollis, at the shriners hospital, mexico city / Tratamento cirúrgico de torcicolo congênito no hospital shriners, cidade do méxico / Tratamiento quirúrgico de tortícolis congénito en el hospital shriners, ciudad de méxico

ABSTRACT Objective: This study aims to evaluate the outcome of surgical treatment of congenital torticollis in our hospital. Methods: We collected the medical records of all patients diagnosed with congenital torticollis in the last 3 years at Shriners Hospital, Mexico City. The cases of congenital torticollis treated with surgery were selected and we evaluated the type of surgical technique, bleeding, time of surgery and complications, as well as the associated diagnoses of hip dysplasia. Results: We found 11 patients, of whom 7 met the inclusion criteria. Three women and four men with mean age of 10.7 years, five of whom had right, and two left side affections. All were surgically treated, five with unipolar and two with bipolar release. The surgery time was similar in both techniques and no complications were found in any of the groups. In two cases there were associated diagnoses, Klippel-Feil syndrome and congenital talipes equinovarus (CTEV) in one and psychomotor retardation in another. No association was found with hip dysplasia. All patients had improved range of movement and head tilt. There were no complications related to the surgical procedure or need for reintervention in our patients. Conclusions: Surgical treatment of congenital torticollis by uni- or bipolar release is an effective and safe method for these patients, presenting aesthetic and functional benefits.

RESUMO Objetivo: Este estudo visa avaliar o resultado do tratamento cirúrgico de torcicolo congênito em nosso hospital. Métodos: Foram coletados os registros de todos os pacientes com diagnóstico de torcicolo congênito nos últimos 3 anos no Hospital Shriners, Cidade do México. Selecionaram-se os casos de torcicolo congênito tratados com cirurgia, avaliando-se tipo de técnica cirúrgica, sangramento, tempo de cirurgias e complicações, assim como os diagnósticos associados e a presença de displasia de quadril. Resultados: Foram encontrados 11 pacientes, dos quais 7 satisfizeram os critérios de inclusão. Três mulheres e quatro homens com média de idade de 10,7 anos, dos quais, cinco tinham afecção do lado direito e dois do lado esquerdo. Todos foram tratados cirurgicamente, cinco com liberação unipolar e dois com bipolar. O tempo de cirurgia foi semelhante nas duas técnicas e não se constataram complicações em nenhum dos grupos. Em dois casos havia diagnósticos associados, síndrome de Klippel-Feil e pé torto equinovaro (PTC) em um e atraso psicomotor em outro. Não se encontrou associação com displasia de quadril. Todos apresentaram melhoras da amplitude de movimento e da inclinação da cabeça. Não houve complicações relacionadas com o procedimento cirúrgico nem necessidade de reintervenção em nossos pacientes. Conclusões: O tratamento cirúrgico do torcicolo congênito por liberação uni ou bipolar é um método efetivo e seguro para esses pacientes, apresentando benefício estético e funcional.

RESUMEN Objetivo: El objetivo de este estudio es evaluar el resultado del tratamiento quirúrgico del tortícolis congénito en nuestro hospital. Métodos: Se recabaron todos los pacientes con diagnóstico de tortícolis congénito en los últimos 3 años en el Hospital Shriners, ciudad de México. Se seleccionaron los casos de tortícolis congénito tratados quirúrgicamente, valorando el tipo de técnica quirúrgica, sangrado, tiempo quirúrgico y complicaciones, así como diagnósticos asociados y la presencia de displasia de cadera. Resultados: Se encontraron 11 pacientes de los cuales 7 cumplieron con los criterios de inclusión. Tres mujeres y cuatro hombres con un promedio de edad de 10.7 años, en los cuales cinco tenían afección en el lado derecho y dos en el izquierdo. Todos fueron manejados quirúrgicamente, cinco con liberación unipolar y dos con bipolar. El tiempo quirúrgico fue similar para las dos técnicas y no se encontraron complicaciones en ninguno de los grupos. En dos casos existieron diagnósticos asociados, síndrome de Klippel-Feil y pie equino varo congénito (PEVC) en uno y retraso psicomotor en otro. No se encontró asociación con displasia de cadera. Todos presentaron mejoría de los arcos de movilidad y de la inclinación de cabeza. No hubo complicaciones relacionadas al procedimiento quirúrgico ni necesidad de reintervenciones en nuestros pacientes. Conclusiones: El tratamiento quirúrgico del tortícolis congénito mediante liberación uni o bipolar es un método efectivo y seguro para estos pacientes, presentando un beneficio estético y funcional.

Vacuum Energy Sequestering and Graviton Loops.

We recently formulated a local mechanism of vacuum energy sequester. This mechanism automatically removes all matter loop contributions to vacuum energy from the stress energy tensor which sources the curvature. Here we adapt the local vacuum energy sequestering mechanism to also cancel all the vacuum energy loops involving virtual gravitons, in addition to the vacuum energy generated by matter fields alone.

Gravitational Mechanisms to Self-Tune the Cosmological Constant: Obstructions and Ways Forward.

Gravitational models of self-tuning are those in which vacuum energy has no observable effect on spacetime curvature, even though it is a priori unsuppressed below the cutoff. We complement Weinberg's no-go theorem by studying field-theoretic completions of self-adjustment allowing for broken translations as well as other generalizations, and identify new obstructions. Our analysis uses a very general Källén-Lehmann spectral representation of the exchange amplitude for conserved sources of energy-momentum and exploits unitarity and Lorentz invariance to show that a transition from self-tuning of long wavelength sources to near general relativity (GR) on shorter scales is generically not possible. We search for novel ways around our obstructions and highlight two interesting possibilities. The first is an example of a unitary field configuration on anti-de Sitter space with the desired transition from self-tuning to GR. A second example is motivated by vacuum energy sequestering.

Manifestly Local Theory of Vacuum Energy Sequestering.

We present a manifestly local, diffeomorphism invariant, and locally Poincaré invariant formulation of vacuum energy sequestering. In this theory, quantum vacuum energy generated by matter loops is canceled by auxiliary fields. The auxiliary fields decouple from gravity almost completely. Their only residual effect is an a priori arbitrary, finite contribution to the curvature of the background geometry, which is radiatively stable. Its value is to be determined by a measurement, like the finite part of any radiatively stable UV-sensitive quantity in quantum field theory.

Sequestration of vacuum energy and the end of the universe.

Recently, we proposed a mechanism for sequestering the standard model vacuum energy that predicts that the Universe will collapse. Here we present a simple mechanism for bringing about this collapse, employing a scalar field whose potential is linear and becomes negative, providing the negative energy density required to end the expansion. The slope of the potential is chosen to allow for the expansion to last until the current Hubble time, about 10^{10} years, to accommodate our Universe. Crucially, this choice is technically natural due to a shift symmetry. Moreover, vacuum energy sequestering selects radiatively stable initial conditions for the collapse, which guarantee that immediately before the turnaround the Universe is dominated by the linear potential which drives an epoch of accelerated expansion for at least an e fold. Thus, a single, technically natural choice for the slope ensures that the collapse is imminent and is preceded by the current stage of cosmic acceleration, giving a new answer to the "why now?"