GenomeScope 2.0 and Smudgeplot for Reference-Free Profiling of Polyploid Genomes

An important assessment prior to genome assembly and related analyses is genome profiling, where the k-mer frequencies within raw sequencing reads are analyzed to estimate major genome characteristics such as size, heterozygosity, and repetitiveness. Here we introduce GenomeScope 2.0 (https://github.com/tbenavi1/genomescope2.0), which applies combinatorial theory to establish a detailed mathematical model of how k-mer frequencies are distributed in heterozygous and polyploid genomes. We describe and evaluate a practical implementation of the polyploid-aware mixture model that quickly and accurately infers genome properties across thousands of simulated and several real datasets spanning a broad range of complexity. We also present a method called Smudgeplot (https://github.com/KamilSJaron/smudgeplot) to visualize and estimate the ploidy and genome structure of a genome by analyzing heterozygous k-mer pairs. We successfully apply the approach to systems of known variable ploidy levels in the Meloidogyne genus and the extreme case of octoploid Fragaria × ananassa

La hipótesis fisicalista en el psicoanálisis freudiano

Freud, de acuerdo a Ernest Jorres, habría mantenido durante toda su vida dos opiniones: 1. No podría existir una psique sin un cerebro. 2. Los procesos físicos deben preceder a los psíquicos. La primera pareciera alejarlo de cualquier hipótesis dualista, y la segunda lo encuadra en un fisicalismo, sin embargo caben distintas interpretaciones en tomo de sus formulaciones: I. Un Fisicalismo reductivo de tipo ontológico. II. Fisicalismo no reductivo ligado a la noción de superveniencia. Se van a analizar estas• interpretaciones de las formulaciones freudianas, y sugerir algunas de las dificultades que comportan al asumir compromisos con otras tesis, no debidamente explicitadas, implicando de alguna manera, en caso de atribuírselas, al psicoanálisis con estas

Mechanisms of copper homeostasis in bacteria

Copper is an important micronutrient required as a redox co-factor in the catalytic centers of enzymes. However, free copper is a potential hazard because of its high chemical reactivity. Consequently, organisms exert a tight control on Cu+ transport (entry-exit) and traffic through different compartments, ensuring the homeostasis required for cuproprotein synthesis and prevention of toxic effects. Recent studies based on biochemical, bioinformatics, and metalloproteomics approaches, reveal a highly regulated system of transcriptional regulators, soluble chaperones, membrane transporters, and target cuproproteins distributed in the various bacterial compartments. As a result, new questions have emerged regarding the diversity and apparent redundancies of these components, their irregular presence in different organisms, functional interactions, and resulting system architectures.Fil: Argüello, José M.. Worcester Polytechnic Institute; Estados UnidosFil: Raimunda, Daniel Cesar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra. Universidad Nacional de Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra; ArgentinaFil: Padilla Benavidez, Teresita. Worcester Polytechnic Institute; Estados Unido

The CFEPS Kuiper Belt Survey: Strategy and Pre-survey Results

We present the data acquisition strategy and characterization procedures for the Canada-France Ecliptic Plane Survey (CFEPS), a sub-component of the Canada-France-Hawaii Telescope Legacy Survey. The survey began in early 2003 and as of summer 2005 has covered 430 square degrees of sky within a few degrees of the ecliptic. Moving objects beyond the orbit of Uranus are detected to a magnitude limit of $m_R$=23 -- 24 (depending on the image quality). To track as large a sample as possible and avoid introducing followup bias, we have developed a multi-epoch observing strategy that is spread over several years. We present the evolution of the uncertainties in ephemeris position and orbital elements as the objects progress through the epochs. We then present a small 10-object sample that was tracked in this manner as part of a preliminary survey starting a year before the main CFEPS project. We describe the CFEPS survey simulator, to be released in 2006, which allows theoretical models of the Kuiper Belt to be compared with the survey discoveries since CFEPS has a well-documented pointing history with characterized detection efficiencies as a function of magnitude and rate of motion on the sky. Using the pre-survey objects we illustrate the usage of the simulator in modeling the classical Kuiper Belt.Comment: to be submitted to Icaru

Sapogenol is a major microbial metabolite in human plasma associated with high protein soy-based diets : the relevance for functional food formulations

Funding: This work was supported by The Scottish Government's Rural and Environment Science and Analytical Services Division (RESAS). Acknowledgments: The authors are grateful to the ALPRO™ Foundation for supporting this work. Author Contributions: Conceptualization, A.M.J. and W.R.R.; methodology, M.N., Y.B., S.H.D., G.J.D., J.S.C.; data curation, M.N.; V.R.; writing—original draft preparation, M.N.; writing—review and editing, M.N.; V.R., W.R.R. All authors have read and agreed to the published version of the manuscript.Peer reviewedPublisher PD

Fluorescent patterning of paper through laser engraving

While thermal treatment of paper can lead to the formation of aromatic structures via hydrothermal treatment (low temperature) or pyrolysis (high temperature), neither of these approaches allow patterning the substrates. Somewhere in between these two extremes, a handful of research groups have used CO2 lasers to pattern paper and induce carbonization. However, none of the previously reported papers have focused on the possibility to form fluorescent derivatives via laser-thermal engraving. Exploring this possibility, this article describes the possibility of using a CO2 laser engraver to selectively treat paper, resulting in the formation of fluorescent compounds, similar to those present on the surface of carbon dots. To determine the most relevant variables controlling this process, 3 MM chromatography paper was treated using a standard 30 W CO2 laser engraver. Under selected experimental conditions, a blue fluorescent pattern was observed when the substrate was irradiated with UV light (365 nm). The effect of various experimental conditions (engraving speed, engraving power, and number of engraving steps) was investigated to maximize the fluorescence intensity. Through a comprehensive characterization effort, it was determined that 5-(hydroxymethyl)furfural and a handful of related compounds were formed (varying in amount) under all selected experimental conditions. To illustrate the potential advantages of this strategy, that could complement those applications traditionally developed from carbon dots (sensors, currency marking, etc.), a redox-based optical sensor for sodium hypochlorite was developed.Fil: Clark, Kaylee M.. Clemson University; Estados UnidosFil: Skrajewski, Lauren. Clemson University; Estados UnidosFil: Benavidez, Tomás Enrique. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; Argentina. Clemson University; Estados UnidosFil: Mendes, Letícia F.. Universidade de Sao Paulo; BrasilFil: Bastos, Erick L.. Universidade de Sao Paulo; BrasilFil: Dörr, Felipe A.. Universidade de Sao Paulo; BrasilFil: Sachdeva, Rakesh. Clemson University; Estados UnidosFil: Ogale, Amod A.. Clemson University; Estados UnidosFil: Paixão, Thiago R. L. C.. Universidade de Sao Paulo; BrasilFil: Garcia, Carlos D.. Clemson University; Estados Unido

Caracterización de sistemas de producción en comunidades rurales de Estelí, Madriz y Nueva Segovia, zona central norte de Nicaragua.

El sector agropecuario y forestal constituye la base de la economía nacional, y de esta depende la seguridad alimentaria familiar en las comunidades rurales. El presente estudio consistió en un diagnóstico de Unidades Productivas en comunidades rurales de nueve municipios del norte de Nicaragua durante el período 2017-2018. Se procesaron 170 encuestas manejada en QUALTRICS por la Santa Clara University, analizadas con softwares especializados, y las variables objeto de análisis descriptivo, univariado y multivariado. Las unidades productivas presentaron áreas menores de 3.51 ha y pocas mayores a 281 ha. El 67 % de los integrantes en las familias mostraron edad menor a 40 años (48.86 % hombres y 50.14 % mujeres). Las familias desarrollaron estrategias de diversificación de rubros y mejorar la seguridad alimentaria, además realizan actividades para enfrentar el cambio climático para mejorar la resiliencia en sus parcelas. Fueron identificadas 54 especies arbóreas agrupadas en 25 familias taxónómicas y conservadas en plantaciones de café bajo sombra. El número de animales, tenencia de la tierra, agua para el hogar y cultivos, café y bosques, características sociales y económicas, problemas y cambio climático, fueron variables discriminantes para relacionar las unidades productivas. Las familias obtienen algunos ingresos de la comercialización de productos; así como trabajo asalariado, pequeños negocios y alquiler de parcelas; no obstante, aún tienen dificultades en asegurar la alimentación durante los meses de junio a agosto

Obonuco San Isidro nueva variedad mejorada de arveja para la zona de reconversión del trigo en Nariño.

El artículo presenta todas las características de la variedad mejorada de arveja, se muestra el origen genético, el comportamiento agronómico, la descripción varietal, la preparación del suelo, la fertilización, el sistema, densidad y época de siembra y el manejo integrado del cultivo como malezas, plagas, enfermedades y cosecha y la conclusión

Obonuco Andina nueva variedad mejorada de arveja para la zona de economía campesina del sur de Nariño.

El artículo presenta todas las características de la variedad mejorada de arveja, se muestra el origen genético, el comportamiento agronómico, los atributos culinarios, las cualidades de mercadeo, la descripción varietal, el manejo agronómico como la preparación del suelo, la fertilización, el sistema, densidad y época de siembra y el manejo de malezas, plagas y enfermedades y las conclusiones.Obonuco Andina, variedad mejorada de arveja para el sistema de economía campesina de Nariñ

The Problem of the Color Line: Spatial Access to Hospital Services for Minoritized Racial and Ethnic Groups

Examining how spatial access to health care varies across geography is key to documenting structural inequalities in the United States. In this article and the accompanying StoryMap, our team identified ZIP Code Tabulation Areas (ZCTAs) with the largest share of minoritized racial and ethnic populations and measured distances to the nearest hospital offering emergency services, trauma care, obstetrics, outpatient surgery, intensive care, and cardiac care. In rural areas, ZCTAs with high Black or American Indian/Alaska Native representation were significantly farther from services than ZCTAs with high White representation. The opposite was true for urban ZCTAs, with high White ZCTAs being farther from most services. These patterns likely result from a combination of housing policies that restrict housing opportunities and federal health policies that are based on service provision rather than community need. The findings also illustrate the difficulty of using a single metric—distance—to investigate access to care on a national scale