Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes.

Metagenomic samples are snapshots of complex ecosystems at work. They comprise hundreds of known and unknown species, contain multiple strain variants and vary greatly within and across environments. Many microbes found in microbial communities are not easily grown in culture making their DNA sequence our only clue into their evolutionary history and biological function. Metagenomic assembly is a computational process aimed at reconstructing genes and genomes from metagenomic mixtures. Current methods have made significant strides in reconstructing DNA segments comprising operons, tandem gene arrays and syntenic blocks. Shorter, higher-throughput sequencing technologies have become the de facto standard in the field. Sequencers are now able to generate billions of short reads in only a few days. Multiple metagenomic assembly strategies, pipelines and assemblers have appeared in recent years. Owing to the inherent complexity of metagenome assembly, regardless of the assembly algorithm and sequencing method, metagenome assemblies contain errors. Recent developments in assembly validation tools have played a pivotal role in improving metagenomics assemblers. Here, we survey recent progress in the field of metagenomic assembly, provide an overview of key approaches for genomic and metagenomic assembly validation and demonstrate the insights that can be derived from assemblies through the use of assembly validation strategies. We also discuss the potential for impact of long-read technologies in metagenomics. We conclude with a discussion of future challenges and opportunities in the field of metagenomic assembly and validation.

[Upper limb functional assessment scale for children with Duchenne muscular dystrophy and Spinal muscular atrophy]. / Escala de evaluación funcional de extremidades superiores en niños con distrofia muscular de Duchenne y Atrofia músculo espinal.

Duchenne muscular dystrophy (DMD) and Spinal muscular atrophy (SMA) causes significant disability and progressive functional impairment. Readily available instruments that assess functionality, especially in advanced stages of the disease, are required to monitor the progress of the disease and the impact of therapeutic interventions. OBJECTIVE: To describe the development of a scale to evaluate upper limb function (UL) in patients with DMD and SMA, and describe its validation process, which includes self-training for evaluators. PATIENTS AND METHOD: The development of the scale included a review of published scales, an exploratory application of a pilot scale in healthy children and those with DMD, self-training of evaluators in applying the scale using a handbook and video tutorial, and assessment of a group of children with DMD and SMA using the final scale. Reliability was assessed using Cronbach and Kendall concordance and with intra and inter-rater test-retest, and validity with concordance and factorial analysis. RESULTS: A high level of reliability was observed, with high internal consistency (Cronbach a = 0.97), and inter-rater (Kendall W = 0.96) and intra-rater concordance (r = 0.97 to 0.99). The validity was demonstrated by the absence of significant differences between results by different evaluators with an expert evaluator (F = 0.023, p > .5), and by the factor analysis that showed that four factors account for 85.44% of total variance. CONCLUSIONS: This scale is a reliable and valid tool for assessing UL functionality in children with DMD and SMA. It is also easily implementable due to the possibility of self-training and the use of simple and inexpensive materials.

Metagenomic Assembly: Overview, Challenges and Applications.

Advances in sequencing technologies have led to the increased use of high throughput sequencing in characterizing the microbial communities associated with our bodies and our environment. Critical to the analysis of the resulting data are sequence assembly algorithms able to reconstruct genes and organisms from complex mixtures. Metagenomic assembly involves new computational challenges due to the specific characteristics of the metagenomic data. In this survey, we focus on major algorithmic approaches for genome and metagenome assembly, and discuss the new challenges and opportunities afforded by this new field. We also review several applications of metagenome assembly in addressing interesting biological problems.

Online learning in the wake of the COVID-19 pandemic: Mixed methods analysis of student views by demographic group.

Various aspects of online learning have been addressed in studies both pre- and during the COVID-19 pandemic. However, most pre-pandemic studies may have suffered from sampling selection issues, as students enrolled in online courses were often not comparable to those taking classes on campus. Similarly, most studies conducted during the initial stages of the pandemic might be confounded by the stress and anxiety associated with worldwide lockdowns and the abrupt switch to online education in most universities. Furthermore, existing studies have not comprehensively explored students' perspectives on online learning across different demographic groups, including gender, race-ethnicity, and domestic versus international student status. To address this research gap, our mixed-methods study examines these aspects using data from an anonymous survey conducted among a large and diverse sample of students at a mid-size university in the Northeastern United States. Our findings reveal important insights: (1) Females are nearly twice as likely as males to prefer online asynchronous classes and feel self-conscious about keeping their cameras on during online synchronous (e.g., Zoom) classes. However, gendered views and preferences align in other aspects of online learning. (2) Black students show a stronger preference for Zoom classes compared to online asynchronous classes and emphasize the importance of recording Zoom meetings. Hispanic students are twice as likely to prefer asynchronous online classes, which offer greater flexibility to manage multiple responsibilities. (3) International students value the ability to learn at their own pace provided by online learning but express dissatisfaction with the lack of peer interaction. On the other hand, domestic students are more concerned about reduced interaction with teachers in online education. Domestic students also exhibit a higher tendency to turn their cameras off during Zoom classes, citing reasons such as self-consciousness or privacy. These findings carry significant implications for future research and educational practice, highlighting the need for tailored approaches that consider diverse student perspectives.

Playful Testing of Executive Functions with Yellow-Red: Tablet-Based Battery for Children between 6 and 11.

Executive functions are psychological processes of great importance for proper functioning in various areas of human development, including academic performance. For this reason, from both clinical and educational perspectives, there is great interest in how they are assessed. This article describes the development and standardization process of Yellow-Red, an instrument for directly assessing executive functions in children between 6 and 11 years of age in a playful format using digital support. The test was based on a three-factor model of executive functioning: inhibition, working memory, and cognitive flexibility. Yellow-Red comprises six subtests: cognitive inhibition, behavioral inhibition, auditory working memory, visual working memory, cognitive flexibility, and a global assessment test of executive functions. The test was administered to 245 boys and girls between 6 and 11 years of age. Along with the Yellow-Red subtests, gold standard tests were applied for each of the executive functions assessed. The test's psychometric properties are powerful in both reliability and validity evidence. The reliability indices are all greater than 0.8. As evidence of convergent validity, correlations were established between the tests, and the tests considered gold standards. All correlations were significant, with values ranging between 0.42 and 0.73. On the other hand, the factor structure of the test was analyzed using confirmatory factor analysis. Although it is possible to demonstrate the progressive differentiation of the factor structure with age, it was only possible to find two factors at older ages, one for inhibition/flexibility and one for working memory.

How did the pandemic affect the socio-emotional well-being of Chilean schoolchildren? A longitudinal study.

This study investigated the repercussions of coronavirus disease (COVID-19) and the subsequent quarantine on the emotional well-being of children in their initial years of formal schooling, with particular emphasis on children with special educational needs (SEN) and children from high and low socioeconomic statuses (SES). This longitudinal study employed the Child Behavior Checklist for ages 6-18 (CBCL) completed by the students' guardians at least once during 2018-2019 and again during 2020. The results showed differences in internalizing and externalizing problems after 8 months of quarantine and a significant increase in students fitting clinical or borderline categories given by the CBCL itself. The results are described in detail for four groups considering the combination of SEN and SES characteristics, showing the importance of their intersectionality, especially between low SES and SEN. (PsycInfo Database Record (c) 2022 APA, all rights reserved).

Deconvoluting complex correlates of COVID-19 severity with a multi-omic pandemic tracking strategy.

The SARS-CoV-2 pandemic has differentially impacted populations across race and ethnicity. A multi-omic approach represents a powerful tool to examine risk across multi-ancestry genomes. We leverage a pandemic tracking strategy in which we sequence viral and host genomes and transcriptomes from nasopharyngeal swabs of 1049 individuals (736 SARS-CoV-2 positive and 313 SARS-CoV-2 negative) and integrate them with digital phenotypes from electronic health records from a diverse catchment area in Northern California. Genome-wide association disaggregated by admixture mapping reveals novel COVID-19-severity-associated regions containing previously reported markers of neurologic, pulmonary and viral disease susceptibility. Phylodynamic tracking of consensus viral genomes reveals no association with disease severity or inferred ancestry. Summary data from multiomic investigation reveals metagenomic and HLA associations with severe COVID-19. The wealth of data available from residual nasopharyngeal swabs in combination with clinical data abstracted automatically at scale highlights a powerful strategy for pandemic tracking, and reveals distinct epidemiologic, genetic, and biological associations for those at the highest risk.

Executive Functions Can Be Improved in Preschoolers Through Systematic Playing in Educational Settings: Evidence From a Longitudinal Study.

This study aimed to test the impact of play on the development of executive functions (EFs) in preschoolers. Thirty-two games were designed to be collectively played in groups by 70 children, in their regular classes. The games were specifically designed to promote the development of the three components of EFs: inhibition (behavioral or cognitive), working memory, and cognitive flexibility. The games focused on each function were of three types: playground games, expression games, and classroom games. Sixty 45 min play sessions were held on consecutive days for 3 months, always in the first period. The sessions were guided by two members of the research team, assisted by the four teachers of the participating classes. The intervention was carried out in two highly socially vulnerable schools in the city of Santiago de Chile. Four classes were studied in total: two experimental groups and two controls. The classes were selected using a questionnaire on teacher-student interaction quality and an age homogeneity criterion. EFs were evaluated using the Hearts and Flowers task at three points: before the intervention (T1), immediately after the end of the intervention (T2), and 8 months after the end of the intervention (T3). The results show a significant difference in the growth of EFs by comparing the experimental and control groups (p = 0.04) between T1 and T3. They also reveal a strong correlation between EFs measures at T1 and mathematics performance at T3. These results are discussed within the context of the guidelines proposed by Diamond and Ling (2016) and Barnett (2011) regarding what an EFs promotion program needs to be considered effective and high quality. The program presented in this study meets most of the requisites mentioned by the authors, which proves that following these guidelines guarantees a high probability of success.

Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018.

The Mid-Atlantic Microbiome Meet-up (M3) organization brings together academic, government, and industry groups to share ideas and develop best practices for microbiome research. In January of 2018, M3 held its fourth meeting, which focused on recent advances in biodefense, specifically those relating to infectious disease, and the use of metagenomic methods for pathogen detection. Presentations highlighted the utility of next-generation sequencing technologies for identifying and tracking microbial community members across space and time. However, they also stressed the current limitations of genomic approaches for biodefense, including insufficient sensitivity to detect low-abundance pathogens and the inability to quantify viable organisms. Participants discussed ways in which the community can improve software usability and shared new computational tools for metagenomic processing, assembly, annotation, and visualization. Looking to the future, they identified the need for better bioinformatics toolkits for longitudinal analyses, improved sample processing approaches for characterizing viruses and fungi, and more consistent maintenance of database resources. Finally, they addressed the necessity of improving data standards to incentivize data sharing. Here, we summarize the presentations and discussions from the meeting, identifying the areas where microbiome analyses have improved our ability to detect and manage biological threats and infectious disease, as well as gaps of knowledge in the field that require future funding and focus.

Ingesta alimentaria y presbifagia en adultos mayores activos de la comunidad de Chillán, Chile / Food intake and presbyphagia in active elderly adults in Chillán, Chile

RESUMEN El propósito del presente estudio fue determinar la prevalencia de presbifagia en adultos mayores que viven en la comunidad y estudiar el estado nutricional e ingesta alimentaria. Material y métodos: Estudio de caso-control con personas mayores de 65 años, pertenecientes a clubes de adultos mayores de Chillán, Chile. La ingesta alimentaria se evaluó a través de la encuesta de tendencia de consumo cuantificada y encuesta de modificación alimentaria creada y validada para este estudio. La presencia de presbifagia se diagnosticó mediante el cuestionario EAT-10 y el diagnóstico de disfagia por MECV-V realizado por fonoaudiólogo. El estado nutricional se evaluó a través del índice de masa corporal. Resultados: La prevalencia de presbifagia fue de 29,5% y disfagia 14,5%. El 74% de los adultos mayores con presbifagia tenía malnutrición por exceso versus 48% de los con disfagia, el 55,5% tenía un cumplimiento insuficiente de energía, situación que no coincide con el estado nutricional predominante de malnutrición por exceso. Las calorías consumidas fueron en base a carbohidratos y proteínas. Tenían una baja ingesta de agua, fibra, calcio y vitamina D y alto consumo de sodio. Los adultos mayores con disfagia demoran más tiempo en comer y han dejado de consumir alimentos que dificultan la deglución como frutas, carnes y arroz. Conclusión: La prevalencia de adultos mayores que viven en la comunidad con presbifagia fue de 29,5%, con malnutrición por exceso en el 74%, para facilitar el proceso deglutorio los adultos mayores con disfagia realizan modificaciones alimentarias a los sólidos.

ABSTRACT The purpose of the present study was to determine the prevalence of presbyphagia in community-living elderly persons and to study nutritional status and dietary intake. Material and methods: We conducted a case-control study with persons over 65 years of age, belonging to clubs for the elderly in Chillán, Chile. Dietary intake was evaluated through a food frequency questionnaire and food modification survey created and validated for this study. Presbyphagia was diagnosed by means of the EAT-10 questionnaire and dysphagia by a speech therapist with MECV-V. The nutritional status was evaluated through the body mass index. Results: The prevalence of presbyphagia was 29.5% and dysphagia 14.5%. 74% of those with presbyphagia had excess malnutrition versus 48% of those with dysphagia, 55.5% had insufficient energy compliance, a situation that does not coincide with the prevailing nutritional status of excess malnutrition. The calories consumed were based on carbohydrates and proteins. They had a low intake of water, fiber, calcium and vitamin D and high sodium in-take. Elderly persons with dysphagia took longer to eat and reported having stopped eating foods difficult to swallow such as fruits, meats and rice. Conclusion: The prevalence of community-living elderly persons with presbyphagia was 29.5% and, among those with presbyphagia, 74% had excess malnutrition. To facilitate the swallowing process, active elderly persons with dysphagia make food modifications to solid food intake.

Escala de evaluación funcional de extremidades superiores en niños con distrofia muscular de Duchenne y Atrofia músculo espinal / Upper limb functional assessment scale for children with Duchenne muscular dystrophy and Spinal muscular atrophy

La distrofia muscular de Duchenne (DMD) y la Atrofia músculo espinal (AME) determinan discapacidad y compromiso funcional progresivo. Se requiere de instrumentos fácilmente disponibles, que evalúen la funcionalidad, especialmente en etapas avanzadas de la enfermedad, para monitorizar evolución e impacto de intervenciones terapéuticas. Objetivo: Reportar el desarrollo de escala para evaluar la función de las extremidades superiores (EESS) en pacientes con DMD y AME, y describir su proceso de validación que incluye autoentrenamiento para evaluadores. Pacientes y Método: El desarrollo de la escala incluyó revisión de escalas publicadas, aplicación exploratoria de escala inicial en niños sanos y con DMD, autoentrenamiento de evaluadores en aplicación de escala definitiva utilizando manual y vídeo tutorial y aplicación de escala en grupo de niños con DMD y AME. Se evaluó confiabilidad con coeficiente de Cronbach y de Kendall y concordancia con test-retest intra e inter-evaluadores, y validez con análisis de concordancia y factorial. Resultados: Se observó alto grado de confiabilidad, con alta consistencia interna (a de Cronbach = 0,97) y concordancia interevaluadores (W de Kendall = 0,96) e intraevaluadores (r = 0,97 a 0,99). La validez se demostró por la inexistencia de diferencias significativas entre resultados de distintos evaluadores con evaluador experto (F = 0,023, p > 0,5) y análisis factorial, que mostró que 4 factores explican el 85,44% de varianza total. Conclusiones: Esta escala de evaluación es un instrumento confiable y válido para evaluar la funcionalidad de EESS en niños con DMD y AME. Además, es de fácil implementación por la posibilidad de autoentrenamiento y el uso de materiales simples y de bajo costo.

Duchenne muscular dystrophy (DMD) and Spinal muscular atrophy (SMA) causes significant disability and progressive functional impairment. Readily available instruments that assess functionality, especially in advanced stages of the disease, are required to monitor the progress of the disease and the impact of therapeutic interventions. Objective: To describe the development of a scale to evaluate upper limb function (UL) in patients with DMD and SMA, and describe its validation process, which includes self-training for evaluators. Patients and Method: The development of the scale included a review of published scales, an exploratory application of a pilot scale in healthy children and those with DMD, self-training of evaluators in applying the scale using a handbook and video tutorial, and assessment of a group of children with DMD and SMA using the final scale. Reliability was assessed using Cronbach and Kendall concordance and with intra and inter-rater test-retest, and validity with concordance and factorial analysis. Results: A high level of reliability was observed, with high internal consistency (Cronbach a = 0.97), and inter-rater (Kendall W = 0.96) and intra-rater concordance (r = 0.97 to 0.99). The validity was demonstrated by the absence of significant differences between results by different evaluators with an expert evaluator (F = 0.023, p > .5), and by the factor analysis that showed that four factors account for 85.44% of total variance. Conclusions: This scale is a reliable and valid tool for assessing UL functionality in children with DMD and SMA. It is also easily implementable due to the possibility of self-training and the use of simple and inexpensive materials.