A computational framework for testing hypotheses of the minimal mechanical requirements for cell aggregation using early annual killifish embryogenesis as a model

Introduction: Deciphering the biological and physical requirements for the outset of multicellularity is limited to few experimental models. The early embryonic development of annual killifish represents an almost unique opportunity to investigate de novo cellular aggregation in a vertebrate model. As an adaptation to seasonal drought, annual killifish employs a unique developmental pattern in which embryogenesis occurs only after undifferentiated embryonic cells have completed epiboly and dispersed in low density on the egg surface. Therefore, the first stage of embryogenesis requires the congregation of embryonic cells at one pole of the egg to form a single aggregate that later gives rise to the embryo proper. This unique process presents an opportunity to dissect the self-organizing principles involved in early organization of embryonic stem cells. Indeed, the physical and biological processes required to form the aggregate of embryonic cells are currently unknown.Methods: Here, we developed an in silico, agent-based biophysical model that allows testing how cell-specific and environmental properties could determine the aggregation dynamics of early Killifish embryogenesis. In a forward engineering approach, we then proceeded to test two hypotheses for cell aggregation (cell-autonomous and a simple taxis model) as a proof of concept of modeling feasibility. In a first approach (cell autonomous system), we considered how intrinsic biophysical properties of the cells such as motility, polarity, density, and the interplay between cell adhesion and contact inhibition of locomotion drive cell aggregation into self-organized clusters. Second, we included guidance of cell migration through a simple taxis mechanism to resemble the activity of an organizing center found in several developmental models.Results: Our numerical simulations showed that random migration combined with low cell-cell adhesion is sufficient to maintain cells in dispersion and that aggregation can indeed arise spontaneously under a limited set of conditions, but, without environmental guidance, the dynamics and resulting structures do not recapitulate in vivo observations.Discussion: Thus, an environmental guidance cue seems to be required for correct execution of early aggregation in early killifish development. However, the nature of this cue (e.g., chemical or mechanical) can only be determined experimentally. Our model provides a predictive tool that could be used to better characterize the process and, importantly, to design informed experimental strategies

The Fourteenth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the extended Baryon Oscillation Spectroscopic Survey and from the second phase of the Apache Point Observatory Galactic Evolution Experiment

The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since July 2014. This paper describes the second data release from this phase, and the fourteenth from SDSS overall (making this, Data Release Fourteen or DR14). This release makes public data taken by SDSS-IV in its first two years of operation (July 2014-2016). Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey (eBOSS); the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data driven machine learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS website (www.sdss.org) has been updated for this release, and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020, and will be followed by SDSS-V.Comment: SDSS-IV collaboration alphabetical author data release paper. DR14 happened on 31st July 2017. 19 pages, 5 figures. Accepted by ApJS on 28th Nov 2017 (this is the "post-print" and "post-proofs" version; minor corrections only from v1, and most of errors found in proofs corrected

Hyperoxemia and excess oxygen use in early acute respiratory distress syndrome : Insights from the LUNG SAFE study

Publisher Copyright: © 2020 The Author(s). Copyright: Copyright 2020 Elsevier B.V., All rights reserved.Background: Concerns exist regarding the prevalence and impact of unnecessary oxygen use in patients with acute respiratory distress syndrome (ARDS). We examined this issue in patients with ARDS enrolled in the Large observational study to UNderstand the Global impact of Severe Acute respiratory FailurE (LUNG SAFE) study. Methods: In this secondary analysis of the LUNG SAFE study, we wished to determine the prevalence and the outcomes associated with hyperoxemia on day 1, sustained hyperoxemia, and excessive oxygen use in patients with early ARDS. Patients who fulfilled criteria of ARDS on day 1 and day 2 of acute hypoxemic respiratory failure were categorized based on the presence of hyperoxemia (PaO2 > 100 mmHg) on day 1, sustained (i.e., present on day 1 and day 2) hyperoxemia, or excessive oxygen use (FIO2 ≥ 0.60 during hyperoxemia). Results: Of 2005 patients that met the inclusion criteria, 131 (6.5%) were hypoxemic (PaO2 < 55 mmHg), 607 (30%) had hyperoxemia on day 1, and 250 (12%) had sustained hyperoxemia. Excess FIO2 use occurred in 400 (66%) out of 607 patients with hyperoxemia. Excess FIO2 use decreased from day 1 to day 2 of ARDS, with most hyperoxemic patients on day 2 receiving relatively low FIO2. Multivariate analyses found no independent relationship between day 1 hyperoxemia, sustained hyperoxemia, or excess FIO2 use and adverse clinical outcomes. Mortality was 42% in patients with excess FIO2 use, compared to 39% in a propensity-matched sample of normoxemic (PaO2 55-100 mmHg) patients (P = 0.47). Conclusions: Hyperoxemia and excess oxygen use are both prevalent in early ARDS but are most often non-sustained. No relationship was found between hyperoxemia or excessive oxygen use and patient outcome in this cohort. Trial registration: LUNG-SAFE is registered with ClinicalTrials.gov, NCT02010073publishersversionPeer reviewe

The Fourteenth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the Extended Baryon Oscillation Spectroscopic Survey and from the Second Phase of the Apache Point Observatory Galactic Evolution Experiment

The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since 2014 July. This paper describes the second data release from this phase, and the 14th from SDSS overall (making this Data Release Fourteen or DR14). This release makes the data taken by SDSS-IV in its first two years of operation (2014–2016 July) public. Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey; the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data-driven machine-learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from the SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS web site (www.sdss.org) has been updated for this release and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020 and will be followed by SDSS-V

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world’s countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome

La revolución en el bicentenario : reflexiones sobre la emancipación, clases y grupos subalternos

La propuesta del Grupo de Trabajo de CLACSO "El Bicentenario Latinoamericano: dos siglos de revoluciones a la luz del presente" consiste en elaborar nuevas perspectivas sobre los dos últimos siglos de historia latinoamericana, problematizando, fundamentalmente, su trayectoria en torno al nudo temático de las revoluciones desde perspectivas interdisciplinarias al interior de las ciencias sociales. Un segundo eje del enfoque propuesto por el Grupo de Trabajo toma en cuenta el papel en esta historia y en este presente, de las clases y sujetos subalternos. Señalamos tres momentos principales: la denominada "primera independencia" (las luchas contra el dominio español), el período del llamado primer centenario y luego de las "revoluciones nacionales" (entre 1904 y 1950 aproximadamente) y los procesos revolucionarios o de lucha contra el dominio de los Estados Unidos, que comprende tanto la fase neoliberal actual y en proyección hacia el Bicentenario como la búsqueda de programa y proyecto latinoamericano y caribeño, comprendiendo incluso el del llamado "socialismo del siglo XXI". Algunas de las preguntas orientadoras de nuestra reflexión son: -¿Qué herencias históricas implicó la condición poscolonial del siglo XXI? -¿Qué determinaciones impuso la inscripción en el mercado capitalista? -¿Qué desafíos significó la presión de los Estados Unidos durane el siglo XX? -¿Cuáles fueron y son las características de los movimientos populares latinoamericanos? -¿Qué promesas y contradicciones singularizaron y singularizan a sus movimientos políticos de corte transformador? -¿Qué novedades políticas y sociales revela el inicio del nuevo siglo? -¿Qué balance es posible realizar del proceso en su conjunto? -¿Qué perspectivas están abiertas para el cambio social latinoamericano? -¿Qué nuevas situaciones supone la conformación de bloques económicos regionales? -¿Existe una forma propia de "revolución latinoamericana"? Esa última es una pregunta decisiva, porque su respuesta define la posibilidad de hablar de una historia y una realidad latinoamericanas. La respuesta puede ser plural e histórica. En este sentido, más que una forma única, investigamos la creación de formas específicas del cambio social, económico, político y cultural. Sin embargo, no es superfluo insistir sobre el interés por construir un enfoque comparativo de la historia latinoamericana. No se trata, entonces, de acumular trabajos monográficos sobre los diferentes países, sino de partir de estudios específicos para compartir preguntas, métodos y problemas para replantear una perspectiva renovada a la luz de las posibilidades actuales. De este modo la celebración del Bicentenario excederá el recuerdo o el festejo para avanzar en una reflexión que retome los proyectos seculares del subcontinente, contribuya a un balance crítico de dos siglos de historia y presente conocimientos para el futuro.Beatriz Rajland y María Celia Cotarelo Presentación | 9 Omar Acha La historia latinoamericana y los procesos revolucionarios: una perspectiva del Bicentenario (1870-2010) | 17 Juan Carlos Gómez Leyton La Revolución en la Historia. Refl exiones sobre el cambio político en América Latina | 39 Luis Suárez Salazar Las utopías Nuestramericanas de la Revolución Cubana: una aproximación histórica | 57 Gerardo Contreras El carácter de las relaciones internacionales: El caso Unión Europea Centroamérica de cara al acuerdo de asociación | 81 Mildred de la Torre Molina La revolución latinoamericana en el proceso nacional cubano (1790-1830) | 95 Daniel Kersffeld Entre evocaciones y desmemorias: México ante su propio Bicentenario | 115 Darío Sarah La construcción de la memoria colectiva del Paraguay: entre el cretinismo y la arcadia perdida | 133 Orietta Favaro y Graciela Iuorno Argentina. Un país a dos velocidades. Provincias y Territorios Nacionales. (1884-1991) | 151 Martha Ruffini El proceso formativo y de consolidación del Estado Argentino en perspectiva histórica. La exclusión política y sus diferentes itinerarios | 169 Ignacio Telesca Desde el revés de la trama: la independencia del Paraguay y los grupos subalternos | 189 J. Alberto Navas Sierra La Revolución atlántica, la independencia americana y La nueva Macro-historia | 209 Felipe de J. Pérez Cruz La educación y la pedagogía cubanas en el movimiento nacional liberador. Visión panorámica desde la revolución en el siglo XIX | 229 Pedro Canales Tapia Parece que no somos felices. Crisis del proyecto oligárquico y movilizaciones indígenas en Latinoamérica, (19001930) | 253 Carmen Rosa Rea Campos Luchas indias en Bolivia: un análisis socio-histórico de la constitución de la política | 273 María Celia Cotarelo La clase obrera en nuestra américa a comienzos del siglo XXI | 291 Steve Cushion Una sublevación de la clase obrera contra el imperio británico | 311 Nicolás Iñigo Carrera Emancipación social y emancipación nacional en el movimiento obrero argentino | 325 José Francisco Puello-Socarrás Revolución sin Guerrillas, ¿guerrillas sin revolución? La vigencia del concepto revolución en las guerrillas contemporáneas. El caso del Ejército de Liberación Nacional en Colombia | 345 Beatriz Rajland y Liliana B. Costante Los nuevos Poderes Constituyentes en la América Latina y Caribeña de hoy y su relación con los procesos de cambio | 367 Angelina Rojas Blaquier El proceso nacional liberador cubano entre 1923 y 1940. Apuntes esenciales | 39