A comprehensive analysis of genome composition and codon usage patterns of emerging coronaviruses

An outbreak of atypical pneumonia caused by a novel Betacoronavirus (βCoV), named SARS-CoV-2 has been declared a public health emergency of international concern by the World Health Organization. In order to gain insight into the emergence, evolution and adaptation of SARS-CoV-2 viruses, a comprehensive analysis of genome composition and codon usage of βCoV circulating in China was performed. A biased nucleotide composition was found for SARS-CoV-2 genome. This bias in genomic composition is reflected in its codon and amino acid usage patterns. The overall codon usage in SARS-CoV-2 is similar among themselves and slightly biased. Most of the highly frequent codons are A- and U-ending, which strongly suggests that mutational bias is the main force shaping codon usage in this virus. Significant differences in relative synonymous codon usage frequencies among SARS-CoV-2 and human cells were found. These differences are due to codon usage preferences.ANII; CSI

Cambiar la mirada sobre el fracaso escolar desde la relación de los jóvenes con el saber

El presente trabajo forma parte del proyecto en curso “Repensar el éxito y el fracaso escolar de la educación secundaria desde la relación de los jóvenes con el saber” (EDU2008-03287), parcialmente financiado por el Ministerio de Educación y Ciencia de España. La finalidad de la investigación es contribuir a incrementar la comprensión sobre como se ha afrontado el éxito y el fracaso en la Escuela Secundaria, a partir del estudio de como los jóvenes se relacionan con el saber (Charlot, 2000) dentro y fuera de la escuela. De las cuatro partes que forman la investigación aquí se presenta los resultados de la primera, donde se exploran las representaciones que guían los estudios realizados desde la aprobación de la LOGSE (1990) en España, y en particular en Cataluña, en torno al éxito y el fracaso escolar. La finalidad de este análisis es ofrecer perspectivas alternativas a lo que se considera como éxito y fracaso escolar, además de propuestas que permitan construir una escuela secundaria inclusiva, en la que todos los estudiantes puedan encontrar su lugar para aprender de los conocimientos, de sí mismos y de los otros

Evidence of increasing diversification of emerging Severe Acute Respiratory Syndrome Coronavirus 2 strains

On 30th January 2020, an outbreak of atypical pneumonia caused by a novelbetacoronavirus, named severe acute respiratory syndrome coronavirus 2(SARS‐CoV‐2), was declared a public health emergency of international concern bythe World Health Organization. For this reason, a detailed evolutionary analysis ofSARS‐CoV‐2 strains currently circulating in different geographic regions of theworld was performed. A compositional analysis as well as a Bayesian coalescentanalysis of complete genome sequences of SARS‐CoV‐2 strains recently isolated inEurope, North America, South America, and Asia was performed. The results ofthese studies revealed a diversification of SARS‐CoV‐2 strains in three differentgenetic clades. Co‐circulation of different clades in different countries, as well asdifferent genetic lineages within different clades were observed. The time of themost recent common ancestor was established to be around 1st November 2019.A mean rate of evolution of 6.57 × 10−4substitutions per site per year was found.A significant migration rate per genetic lineage per year from Europe to SouthAmerica was also observed. The results of these studies revealed an increasingdiversification of SARS‐CoV‐2 strains. High evolutionary rates and fast populationgrowth characterizes the population dynamics of SARS‐CoV‐2 strains

A maturity model for the information-driven SME

Purpose: This article presents a maturity model for the evaluation of the information-driven decision-making process (DMP) in small and medium enterprises. This model is called “Simplified Holistic Approach to DMP Evaluation (SHADE)”. The SHADE model is based in the “Circumplex Hierarchical Representation of the Organization Maturity Assessment” (CHROMA) framework for characterizing the information-driven DMP in organizations Design/methodology/approach: The CHROMA-SHADE provides a competency evaluation methodology regarding the SME’s use of data for making better-informed decisions. This model groups the main factors influencing the information-driven DMP and classifies them into five dimensions: data availability, data quality, data analysis and insights, information use and decision-making. It addresses these dimensions systematically, delivering a framework for positioning the organization from an uninitiated to a completely embedded stage. The assessment consists of interviews based on a standardized open-ended questionnaire performed to key company personnel followed by an analysis of the answers and their scoring performed by an expert evaluator. Findings: The results of its application indicate this model is well adapted to the SMEs resulting useful for identifying strengths and weaknesses, thereby providing insights for prioritizing improvement actions. Originality/value: The CHROMA-SHADE model follows a novel, holistic approach that embraces the complexities inherent in a multiplicity of factors that, at the technological and management level, converge to enable more objective and better-supported decisions to be made through the intelligent use of information.Peer Reviewe

Chronological evolution of the information-driven decision-making process (1950–2020)

The version of record os available online at:https://doi.org/10.1007/s13132-022-00917-yThe decision-making process (DMP) is essential in organizations and has changed due to multidisciplinary research, greatly infuenced by the progress in information technologies and computational science. This work’s objective is analysing the progressive interaction between DMP and information technologies and the consequent breakthroughs in how business is conducted since 1950 to recent times. Therefore, a chronological review of the information-driven DMP evolvement is presented. The major landmarks that defned how technology infuenced how information is generated, stored, managed, and used for making better decisions, minimizing the uncertainty and gaining knowledge, are covered. The fndings showed that even if current data-driven trends in managerial decision making have led to competitive advantages and business opportunities, there is still a gap between the technological capabilities and the organizational needs. Nowadays, it has been reported that the adoption of technology solutions in many companies is faster than their capacity to adapt at managerial level. Aware of this reality, the “Circumplex Hierarchical Representation of Organization Maturity Assessment” (CHROMA) model has been developed. This tool makes it possible to evaluate whether the management of organizations is making decisions using the available data correctly and optimizing their information systems.Peer ReviewedPostprint (published version

Nuevo sistema de doble-paso compacto con enfoque asimétrico

Every day more people are using multifocal systems to correct presbyopia, as for example contact lenses or intraocular lenses. As a consequence, the necessity to do an appropriate characterization of their optical quality has increased. Due to this situation, the main purpose of this project has been to develop a new compact open-field double-pass system with asymmetric focus that characterizes objectively in vivo the optical quality of multifocal systems that are adapted or implanted in the eye. As a preliminary study, one diffractive and one refractive multifocal lens were implanted in a wet customized model-eye and characterized by this new set-up. Regarding the asymmetric focus of the set-up, a through-focus from +0.75 to -4.00D in steps of 0.25D was performed in the second pass for each tested lens,while the optical power of the first pass remained fixed. Results show that it is possible to distinguish, characterize the different foci of the measured multifocal intraocular lenses implanted in the model eye, and evaluate the optical quality of the system composed by the eye + the multifocal element. Therefore, it has been concluded that this new compact open-field double-pass system with asymmetric focus is suitable to evaluate the optical quality of multifocal systems adapted or implanted in the eye.Cada día más personas usan elementos ópticos multifocales para corregir la presbicia, por ejemplo una lente de contacto o una lente intraocular. En consecuencia, la necesidad de evaluar la calidad óptica del ojo con un elemento corrector multifocal ha adquirido una gran importancia. Dada esta situación, el principal objetivo de este proyecto ha sido desarrollar un nuevo sistema compacto basado en la técnica de doble-paso con enfoque asimétrico capaz de realizar una caracterización objetiva e “in vivo” de la calidad óptica del conjunto ojo-elemento óptico multifocal. En este estudio preliminar se han empleado dos lentes intraoculares multifocales, una difractiva y otra refractiva,implantadas en un ojo artificial. Al ser un sistema con enfoque asimétrico, se utilizó el segundo paso para realizar un barrido desde +0.75 a -4.00D en pasos de 0.25 D manteniendo el primer paso fijo. Los resultados han mostrado que es posible hallar y diferenciar los dos planos de enfoque, lejano y cercano, de las lentes intraoculares multifocales implantadas en el ojo artificial y evaluar la calidad óptica del conjunto ojoelemento multifocal. Por tanto, se ha demostrado la viabilidad de este nuevo sistema compacto de doble-paso con enfoque asimétrico para caracterizar la calidad óptica de un ojo con un elemento óptico multifocal.Postprint (published version

Maturity model for the information-driven SME

Purpose: This article presents a maturity model for the evaluation of the information-driven decision-making process (DMP) in small and medium enterprises. This model is called “Simplified Holistic Approach to DMP Evaluation (SHADE)”. The SHADE model is based in the “Circumplex Hierarchical Representation of the Organization Maturity Assessment” (CHROMA) framework for characterizing the information-driven DMP in organizations Design/methodology/approach: The CHROMA-SHADE provides a competency evaluation methodology regarding the SME’s use of data for making better-informed decisions. This model groups the main factors influencing the information-driven DMP and classifies them into five dimensions: data availability, data quality, data analysis and insights, information use and decision-making. It addresses these dimensions systematically, delivering a framework for positioning the organization from an uninitiated to a completely embedded stage. The assessment consists of interviews based on a standardized open-ended questionnaire performed to key company personnel followed by an analysis of the answers and their scoring performed by an expert evaluator. Findings: The results of its application indicate this model is well adapted to the SMEs resulting useful for identifying strengths and weaknesses, thereby providing insights for prioritizing improvement actions. Originality/value: The CHROMA-SHADE model follows a novel, holistic approach that embraces the complexities inherent in a multiplicity of factors that, at the technological and management level, converge to enable more objective and better-supported decisions to be made through the intelligent use of informatio

Lung ultrasound as a predictor of mortality of patients with Covid-19

Objective: To evaluate the performance of lung ultrasound to determine short-term outcomes of patients with COVID-19 admitted to the intensive care unit. Methods: This is a Prospective, observational study. Between July and November 2020, 59 patients were included and underwent at least two LUS assessments using LUS score (range 0-42) on day of admission, day 5th, and 10th of admission. Results: Age was 66.5±15 years, APACHE II was 8.3±3.9, 12 (20%) patients had malignancy, 46 (78%) patients had a non‑invasive ventilation/high-flow nasal cannula and 38 (64%) patients required mechanical ventilation. The median stay in ICU was 12 days (IQR 8.5-20.5 days). ICU or hospital mortality was 54%. On admission, the LUS score was 20.8±6.1; on day 5th and day 10th of admission, scores were 27.6±5.5 and 29.4±5.3, respectively (P=0.007). As clinical condition deteriorated the LUS score increased, with a positive correlation of 0.52, P <0.001. Patients with worse LUS on day 5th versus better score had a mortality of 76% versus 33% (OR 6.29, 95%CI 2.01-19.65, p. 0.003); a similar difference was observed on day 10. LUS score of 5th day of admission had an area under the curve of 0.80, best cut-point of 27, sensitivity and specificity of 0.75 and 0.78 respectively. Conclusion: These findings position LUS as a simple and reproducible method to predict the course of COVID-19 patients.Fil: Sosa, Fernando A.. Hospital Alemán; ArgentinaFil: Matarrese, Agustín. Hospital Aleman; ArgentinaFil: Saavedra, Santiago. Hospital Aleman; ArgentinaFil: Osatnik, Javier. Hospital Alemán; ArgentinaFil: Roberti, Javier Eugenio. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Centro de Investigaciones en Epidemiología y Salud Pública. Instituto de Efectividad Clínica y Sanitaria. Centro de Investigaciones en Epidemiología y Salud Pública; ArgentinaFil: Tort Oribe, Barbara. Hospital Alemán; ArgentinaFil: Ivulich, Daniel. Hospital Aleman; ArgentinaFil: Durán, Ana Laura. Hospital Alemán; ArgentinaFil: Caputo, Celeste. Hospital Aleman; ArgentinaFil: Benay, Cristian Gabriel. Hospital Alemán; Argentin

Survey of transcripts expressed by the invasive juvenile stage of the liver fluke Fasciola hepatica

<p>Abstract</p> <p>Background</p> <p>The common liver fluke <it>Fasciola hepatica </it>is the agent of a zoonosis with significant economic consequences in livestock production worldwide, and increasing relevance to human health in developing countries. Although flukicidal drugs are available, re-infection and emerging resistance are demanding new efficient and inexpensive control strategies. Understanding the molecular mechanisms underlying the host-parasite interaction provide relevant clues in this search, while enlightening the physiological adaptations to parasitism. Genomics and transcriptomics are still in their infancy in <it>F. hepatica</it>, with very scarce information available from the invasive newly excysted juveniles (NEJ). Here we provide an initial glimpse to the transcriptomics of the NEJ, the first stage to interact with the mammalian host.</p> <p>Results</p> <p>We catalogued more than 500 clusters generated from the analysis of <it>F. hepatica </it>juvenile expressed sequence tags (EST), several of them not detected in the adult stage. A set of putative <it>F. hepatica </it>specific transcripts, and a group of sequences conserved exclusively in flatworms were identified. These novel sequences along with a set of parasite transcripts absent in the host genomes are putative new targets for future anti-parasitic drugs or vaccine development.</p> <p>Comparisons of the <it>F. hepatica </it>sequences with other metazoans genomes or EST databases were consistent with the basal positioning of flatworms in the bilaterian phylogeny. Notably, GC content, codon usage and amino acid frequencies are remarkably different in Schistosomes to <it>F. hepatica </it>and other trematodes.</p> <p>Functional annotation of predicted proteins showed a general representation of diverse biological functions. Besides proteases and antioxidant enzymes expected to participate in the early interaction with the host, various proteins involved in gene expression, protein synthesis, cell signaling and mitochondrial enzymes were identified. Differential expression of secreted protease gene family members between juvenile and adult stages may respond to different needs during host colonization.</p> <p>Conclusion</p> <p>The knowledge of the genes expressed by the invasive stage of <it>Fasciola hepatica </it>is a starting point to unravel key aspects of this parasite's biology. The integration of the emerging transcriptomics, and proteomics data and the advent of functional genomics tools in this organism are positioning <it>F. hepatica </it>as an interesting model for trematode biology.</p

Survey of transcripts expressed by the invasive juvenile stage of the liver fluke Fasciola hepatica

<p>Abstract</p> <p>Background</p> <p>The common liver fluke <it>Fasciola hepatica </it>is the agent of a zoonosis with significant economic consequences in livestock production worldwide, and increasing relevance to human health in developing countries. Although flukicidal drugs are available, re-infection and emerging resistance are demanding new efficient and inexpensive control strategies. Understanding the molecular mechanisms underlying the host-parasite interaction provide relevant clues in this search, while enlightening the physiological adaptations to parasitism. Genomics and transcriptomics are still in their infancy in <it>F. hepatica</it>, with very scarce information available from the invasive newly excysted juveniles (NEJ). Here we provide an initial glimpse to the transcriptomics of the NEJ, the first stage to interact with the mammalian host.</p> <p>Results</p> <p>We catalogued more than 500 clusters generated from the analysis of <it>F. hepatica </it>juvenile expressed sequence tags (EST), several of them not detected in the adult stage. A set of putative <it>F. hepatica </it>specific transcripts, and a group of sequences conserved exclusively in flatworms were identified. These novel sequences along with a set of parasite transcripts absent in the host genomes are putative new targets for future anti-parasitic drugs or vaccine development.</p> <p>Comparisons of the <it>F. hepatica </it>sequences with other metazoans genomes or EST databases were consistent with the basal positioning of flatworms in the bilaterian phylogeny. Notably, GC content, codon usage and amino acid frequencies are remarkably different in Schistosomes to <it>F. hepatica </it>and other trematodes.</p> <p>Functional annotation of predicted proteins showed a general representation of diverse biological functions. Besides proteases and antioxidant enzymes expected to participate in the early interaction with the host, various proteins involved in gene expression, protein synthesis, cell signaling and mitochondrial enzymes were identified. Differential expression of secreted protease gene family members between juvenile and adult stages may respond to different needs during host colonization.</p> <p>Conclusion</p> <p>The knowledge of the genes expressed by the invasive stage of <it>Fasciola hepatica </it>is a starting point to unravel key aspects of this parasite's biology. The integration of the emerging transcriptomics, and proteomics data and the advent of functional genomics tools in this organism are positioning <it>F. hepatica </it>as an interesting model for trematode biology.</p