92 research outputs found

    Estudios de Patogenicidad de Viroides del Género Apscaviroide y Hostuviroide en cítricos

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    Estudios realizados en Atalantia citroides, un género afín de los cítricos, mostraron que estaba infectada con un viroide no descrito hasta el momento. Este nuevo viroide tiene un genoma de 293-294 nucleótidos con una alta proporción de bases GC, una región central conservada que es característica de los miembros del género Apscaviroid, y también la región terminal conservada que tienen este y otros géneros de la familia Pospiviroidae. La estructura secundaria de mínima energía libre predicha para este nuevo viroide es una conformación en forma de varilla con un 68.7% de nucleótidos apareados y con una identidad de secuencia respecto a los otros viroides inferior al 90%, que es el límite convenido para separar las diferentes especies de viroides dentro de un mismo género. Los ensayos de infectividad utilizando el cidro Etrog han mostrado que este nuevo viroide produce síntomas característicos suaves. La co-inoculació de este nuevo viroide con Citrus bent leaf viroid o con Citrus dwarfing viroid, que también son miembros del género Apscaviroid, causa interacciones sinérgicas que se manifiestan induciendo síntomas muy pronunciados en las hojas y un enanismo muy marcado. Este aumento en la intensidad de síntomas no está acompañado por variaciones en la acumulación del viroide en la planta ya que su concentración se mantiene inalterada en plantas co-inoculadas. De acuerdo con estas propiedades moleculares y biológicas, así como por su capacidad por replicarse en A. citroides, este nuevo viroide que tentativamente hemos nombrado Citrus viroid V (CVd-V), ha sido propuesto como una nueva especie del género Apscaviroid. El análisis de 64 muestras provenientes de varias zonas citrícolas ha mostrado que CVd-V está presente en los Estados Unidos, España Nepal, y el Sultanato de Oman. Estos resultados indican que este viroide no ha surgido recientemente y está bastante difundido por diferentes partes del mundo. Los ensayos de transmisión a naranjo, mandarino, híbSerra Alfonso, P. (2009). Estudios de Patogenicidad de Viroides del Género Apscaviroide y Hostuviroide en cítricos [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/6028Palanci

    Apple hammerhead viroid-like RNA is a bona fide viroid: Autonomous replication and structural features support its inclusion as a new member in the genus Pelamoviroid

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    [EN] Apple hammerhead viroid-like RNA (AHVd RNA) has been reported in different apple cultivars and geographic regions and, considering the presence of hammerhead ribozymes in both polarity strands, suspected to be either a viroid of the family Avsunviroidae or a viroid-like satellite RNA. Here we report that dimeric head-to-tail in vitro transcripts of a 433-nt reference variant of AHVd RNA from cultivar "Pacific Gala" are infectious when mechanically inoculated to apple, thus showing that this RNA is a bona fide viroid for which we have kept the name apple hammerhead viroid (AHVd) until its pathogenicity, if any, is better assessed. By combining thermodynamics-based predictions with co-variation analyses of the natural genetic diversity found in AHVd we have inferred the most likely conformations for both AHVd polarity strands in vivo, with that of the (+) polarity strand being stabilized by a kissing loop-interaction similar to those reported in peach latent mosaic viroid and chrysathemum chlorotic mottle viroid, the two known members of the genus Pelamoviroid (family Avsunviroidae). Therefore, AHVd RNA fulfills the biological and molecular criteria to be allocated to this genus, the members of which, intriguingly, display low global sequence identity but high structural conservation.We wish to express our gratitude to Dr. Marcos de la Pefia for valuable suggestions, to Maria Pedrote for excellent technical assistance, and to Dr. Miguel Cambra for facilitating access to the apple material. This research was partly funded by grant BFU2014-56812-P (to R.F.) from the Ministerio de Economia y Competitividad (MINECO) of Spain (which included a posdoctoral contract for P.S.), and by the Canadian Food Inspection Agency's Plant Research and Strategies Technology Development (TD) Program (to D.J.).Serra Alfonso, P.; Messmer, A.; Sanderson, D.; James, D.; Flores Pedauye, R. (2018). Apple hammerhead viroid-like RNA is a bona fide viroid: Autonomous replication and structural features support its inclusion as a new member in the genus Pelamoviroid. Virus Research. 249:8-15. https://doi.org/10.1016/j.virusres.2018.03.001S81524

    Interference between variants of peach latent mosaic viroid reveals novel features of its fitness landscape: implications for detection

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    [EN] Natural populations of peach latent mosaic viroid (PLMVd) are complex mixtures of variants. During routine testing, TaqMan rtRT-PCR and RNA gel-blot hybridization produced discordant results with some PLMVd isolates. Analysis of the corresponding populations showed that they were exclusively composed of variants (of class II) with a structural domain different from that of the reference and many other variants (of class I) targeted by the TaqMan rtRT-PCR probe. Bioassays in peach revealed that a representative PLMVd variant of class II replicated without symptoms, generated a progeny with low nucleotide diversity, and, intriguingly, outcompeted a representative symptomatic variant of class I when co-inoculated in equimolecular amounts. A number of informative positions associated with the higher fitness of variants of class II have been identified, and novel sets of primers and probes for universal or specific TaqMan rtRT-PCR detection of PLMVd variants have been designed and tested.We thank A. Ahuir for excellent technical assistance and Dr. Francesco Di Serio for suggestions. This work was supported by grant BFU2014-56812-P (to R.F.) from Ministerio de Economia y Competitividad (MINECO) of Spain. P.S. was the recipient of a postdoctoral contract from MINECO and E. Bertolini of an INIA-CCA2011-2016 contract also from MINECO.Serra Alfonso, P.; Bertolini, E.; Martinez, MC.; Cambra, M.; Flores Pedauye, R. (2017). Interference between variants of peach latent mosaic viroid reveals novel features of its fitness landscape: implications for detection. Scientific Reports. 7. https://doi.org/10.1038/srep42825S7Diener, T. O. Discovering viroids - a personal perspective. Nat. Rev. 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A novel multiplex RT-PCR probe capture hybridization (RT-PCR-ELISA) for simultaneous detection of six viroids in four genera: Apscaviroid, Hostuviroid, Pelamoviroid, and Pospiviroid . J. Virol. Methods 105, 115–121 (2002).Ragozzino, E., Faggioli, F. & Barba, M. Development of a one tube-one step RT-PCR protocol for the detection of seven viroids in four genera: Apscaviroid, Hostuviroid, Pelamoviroid and Pospiviroid. J. Virol. Methods 121, 25–29 (2004).Luigi, M. & Faggioli, F. Development of quantitative real-time RT-PCR for the detection and quantification of peach latent mosaic viroid. Eur. J. Plant Pathol. 130, 109–116 (2011).Parisi, O., Lepoivre, P. & Jijakli, M. H. Development of a quick quantitative real-time PCR for the in vivo detection and quantification of peach latent mosaic viroid. Plant Dis. 95, 137–142 (2011).Lin, L., Li, R., Bateman, M., Mock, R. & Kinard, G. Development of a multiplex TaqMan real-time RT-PCR assay for simultaneous detection of Asian prunus viruses, plum bark necrosis stem pitting associated virus, and peach latent mosaic viroid. Eur. J. Plant Pathol. 137, 797–804 (2013).Zhang, Y. J. et al. A universal oligonucleotide microarray with a minimal number of probes for the detection and identification of viroids at the genus level. PLoS One 8, e64474 (2013).Di Serio, F. et al. Deep sequencing of the small RNAs derived from two symptomatic variants of a chloroplastic viroid: implications for their genesis and for pathogenesis. PLoS One 4, e7539 (2009).Bolduc, F., Hoareau, C., St-Pierre, P. & Perreault, J. P. In-depth sequencing of the siRNAs associated with peach latent mosaic viroid infection. BMC Mol. Biol. 11, 16 (2010).Glouzon, J. P. S., Bolduc, F., Wang, S., Najmanovich, R. J. & Perreault, J. P. Deep-sequencing of the peach latent mosaic viroid reveals new aspects of population heterogeneity. 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    Viroids: from genotype to phenotype just relying on RNA sequence and structural motifs

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    [EN] As a consequence of two unique physical properties, small size and circularity, viroid RNAs do not code for proteins and thus depend on RNA sequence/structural motifs for interacting with host proteins that mediate their invasion, replication, spread, and circumvention of defensive barriers. Viroid genomes fold up on themselves adopting collapsed secondary structures wherein stretches of nucleotides stabilized by Watson Crick pairs are flanked by apparently unstructured loops. However, compelling data show that they are instead stabilized by alternative non canonical pairs and that specific loops in the rod like secondary structure, characteristic of Potato spindle tuber viroid and most other members of the family Pospiviroidae, are critical for replication and systemic trafficking. In contrast, rather than folding into a rod-like secondary structure, most members of the family Avsunviroidae adopt multibranched conformations occasionally stabilized by kissing-loop interactions critical for viroid viability in vivo. Besides these most stable secondary structures, viroid RNAs alternatively adopt during replication transient metastable conformations containing elements of local higher-order structure, prominent among which are the hammerhead ribozymes catalyzing a key replicative step in the family Avsunviroidae, and certain conserved hairpins that also mediate replication steps in the family Pospiviroidae. Therefore, different RNA structures either global or local determine different functions, thus highlighting the need for in-depth structural studies on viroid RNAs.We thank Dr. J. A. Daros for critical reading and suggestions, Dr. B. Ding for kindly providing Figures 4 and 5, and Dr. M. de la Pena for kindly providing Figure 6. Research in Ricardo FLores laboratory is presently supported by grant BFU2011-28443 from the Ministerio de Educacion y Ciencia (MEC) of Spain. During this work Pedro Serra has been supported by postdoctoral contracts from the Generalitat Valenciana (APOSTD/2010, program VALi+d) and the MEC (program Juan de la Cierva), and Sofia Minoia by a predoctoral fellowship from the MEC.Flores Pedauye, R.; Serra Alfonso, P.; Minoia, S.; Di Serio, F.; Navarro, B. (2012). Viroids: from genotype to phenotype just relying on RNA sequence and structural motifs. Frontiers in Microbiology. 3:217-1-217-13. https://doi.org/10.3389/fmicb.2012.00217S217-1217-13

    Aprendizaje cooperativo y mapas conceptuales

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    En la elaboración de este libro también participaron los siguientes estudiantes: Barreda Santa Cruz, Begoña / Palau Nos, Jorge / Lerma Poveda, Carlos / Zuco Monaco, Paolo / Bolta Miñana, Borja / Entraigas García, Carla / Risueño Martí, Jorge / Cortés Aparisi, Raquel / Díaz Megías, Mónica / Garrigós Padilla, María / Jiménez del Valle Natalia / Morales San Martín Cristina / Navarro Ahullana, Mar / Navarro López, María / Peraire Besalduch, Angela / James Harrison / Rebecca Spencer / Hannah Westcott / María Cholvi Gil / Carlota Clemente Almendros / María Ibáñez Beltrán / Jorge Pastor Panadero / María del Pilar Ventura Salvador / Mario Rodríguez Molero / Pablo Alba Repullo / Teresa Pérez Huertas / Jorge Alarcón Fernández / Rodrigo Climent Pedrosa / Christian de Joz Latorre / Marina Muñoz Máyquez / Samuel Ezquerro Lalinde / Sandra Aponte Fernandez / Victoria Salguero Rebolledo / Andrés Martinez Lopera / Jorge Garcia oragues / José Mª De Vicente Garcia / Nacho Rivaya Martos / Eduardo Fabado Alfaro / Manuel Pando Cáceres / Miriam Franch Citoler / Lucía López López / Patricia Sabater Tortajada / Andrea Serra Pla / Elisabeth Ruiz Perez / Inmaculada Concepción Ortiz Bella / Daniel Climent de la Guia / David Lozano Pellicer / Nuria Cerdà Moreno / Raquel Cervera Martín / Laura Gutiérrez Trujillo / Nerea Lopez Arribas / Sheyla Martorell Luján / Jorge Almenar Ruiz / Marta García Espallarga / Miguel Medina Melián / Luis Parra Martínez / Anna Spuche Catalunya / Rafael Villalba Crucera / Cristina Guerrero Fabra / Consuelo Verdú Belando / Cristina Gabaldón Cuenca / Alba Segarra Villar / Silvia Martínez Rocher / María González Marimón / Irene Grima Simón / Ana Carbonell Garrido / Elisenda Gómez Mele / Clara Teresa Latorre Salvador / Esperanza Llavata Silva / Aitana Muñoz Martí / Daniel Rocher Camps / José Antonio Lopez De La Isidra Aguilar / Francisco Javier Rodriguez Urbano / Rafael Gimenez Minguez / Mª Teresa Martínez Casalí / Alfonso Martínez-Bernal Herrero / Patricia Navarro Pla / Sandra Soto Vozmediano / Mª Antonia García Juncos / Natalia Hernández Roldán / Soraya Hinarejos Carrasco / Merche Moncholí Fernández / Amparo Ros Gimeno / Patricia Martínez Viana / Bruno Benedito Pérez / Joan Enguer Saus / Pablo Palomar Muñoz / Joaquín Server Martorell / María Amparo Monasor Pérez / Ángela Ruiz López / Naiara Ramos Gil / Antonio Santiago Muñoz / Soraya Sánchez Baixauli / Carlota Ramírez PérezEl Libro cuenta con dos partes unidas por un punto común, los mapas conceptuales como metodología docente activa para los estudios de Grado en Derecho. En la Parte General se expone la visión del profesorado del aprendizaje cooperativo y la inserción de los mapas conceptuales como metodología activa en los estudios y aprendizaje del Derecho, mientas que en la Parte Especial se expone la visión estudiantil de los mapas conceptuales. Finalmente el Libro cuenta con un Anexo donde aparecen los mapas elaborados por los estudiantes.El libro forma parte de los resultados del Proyecto de Investigación de Finestra Oberta Tipo del Proyecto / Finestra Oberta Proyecto de Innovación que dirige la Coordinadora de la obra Profesora Cobas Cobiella Concedido en el curso 2012-2013 UV-SFPIE_ FO12-8082

    Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia

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    Chronic lymphocytic leukemia (CLL) has heterogeneous clinical and biological behavior. Whole-genome and -exome sequencing has contributed to the characterization of the mutational spectrum of the disease, but the underlying transcriptional profile is still poorly understood. We have performed deep RNA sequencing in different subpopulations of normal B-lymphocytes and CLL cells from a cohort of 98 patients, and characterized the CLL transcriptional landscape with unprecedented resolution. We detected thousands of transcriptional elements differentially expressed between the CLL and normal B cells, including protein-coding genes, noncoding RNAs, and pseudogenes. Transposable elements are globally derepressed in CLL cells. In addition, two thousand genes-most of which are not differentially expressed-exhibit CLL-specific splicing patterns. Genes involved in metabolic pathways showed higher expression in CLL, while genes related to spliceosome, proteasome, and ribosome were among the most down-regulated in CLL. Clustering of the CLL samples according to RNA-seq derived gene expression levels unveiled two robust molecular subgroups, C1 and C2. C1/C2 subgroups and the mutational status of the immunoglobulin heavy variable (IGHV) region were the only independent variables in predicting time to treatment in a multivariate analysis with main clinico-biological features. This subdivision was validated in an independent cohort of patients monitored through DNA microarrays. Further analysis shows that B-cell receptor (BCR) activation in the microenvironment of the lymph node may be at the origin of the C1/C2 differences

    A structural biology community assessment of AlphaFold2 applications

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    Most proteins fold into 3D structures that determine how they function and orchestrate the biological processes of the cell. Recent developments in computational methods for protein structure predictions have reached the accuracy of experimentally determined models. Although this has been independently verified, the implementation of these methods across structural-biology applications remains to be tested. Here, we evaluate the use of AlphaFold2 (AF2) predictions in the study of characteristic structural elements; the impact of missense variants; function and ligand binding site predictions; modeling of interactions; and modeling of experimental structural data. For 11 proteomes, an average of 25% additional residues can be confidently modeled when compared with homology modeling, identifying structural features rarely seen in the Protein Data Bank. AF2-based predictions of protein disorder and complexes surpass dedicated tools, and AF2 models can be used across diverse applications equally well compared with experimentally determined structures, when the confidence metrics are critically considered. In summary, we find that these advances are likely to have a transformative impact in structural biology and broader life-science research

    Bariatric surgery: evidence-based practical recommendations

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    [Resumen] La obesidad mórbida es, habitualmente, refractaria a los tratamientos convencionales, por lo que la modificación de hábitos dietéticos y de actividad física y/o el uso de fármacos consiguen pérdidas de peso parciales con habitual recuperación posterior. La cirugía bariátrica constituye una opción terapéutica para los casos de obesidad con elevado índice de masa corporal (IMC) asociada a comorbilidades, con buenos resultados a corto y largo plazo. El Grupo de Trabajo sobre Obesidad de la Sociedad Española de Endocrinología y Nutrición (GOSEEN) ha elaborado un documento con recomendaciones prácticas basadas en la evidencia para el tratamiento quirúrgico de la obesidad. La revisión se estructura en 3 partes. En la primera se definen los conceptos de obesidad y comorbilidades asociadas, los tratamientos médicos y sus resultados, las indicaciones y contraindicaciones para el tratamiento quirúrgico con los criterios de selección de los pacientes, el manejo pre y perioperatorio y la valoración de grupos especiales, como adolescentes y personas de edad avanzada. En la segunda parte se describen las distintas técnicas quirúrgicas, las vías de acceso y los resultados comparativos, las complicaciones tanto a corto como a largo plazo, la repercusión de la pérdida ponderal sobre las comorbilidades y los criterios para evaluar la efectividad de la cirugía. En la tercera parte se desarrolla el seguimiento postoperatorio, el control dietético en fases tempranas y más tardías tras la cirugía, y el calendario de control médico y analítico con la suplementación de los distintos macro y micronutrientes en función de la técnica quirúrgica empleada. Se incluye un apartado final sobre gestación y cirugía bariátrica, así como tablas y gráficos complementarios al texto desarrollado. La cirugía bariátrica sigue siendo un tratamiento discutido para la obesidad, pero los resultados en la corrección del exceso ponderal con mejoría en las patologías asociadas y en la calidad de vida confirman que puede ser el tratamiento de elección en pacientes seleccionados, con la técnica quirúrgica apropiada y con un correcto control pre y postoperatorio.[Abstract] Morbid obesity is usually refractory to conventional treatments. Consequently, weight that is lost by modifying diet and exercise and/or the use of drugs is usually later regained. Bariatric surgery constitutes a therapeutic option in obese patients with a high body mass index associated with comorbidities and achieves good results in both the short and the long term. The Obesity Working Group of the Spanish Society of Endocrinology and Nutrition has produced a document with practical, evidencebased recommendations for the surgical treatment of obesity. The review is structured in three parts. The first part defines the concepts of obesity and associated comorbidities, medical treatments, their results, and the indications and contraindications for surgical treatment, as well as the criteria for patient selection, pre- and perisurgical management, and assessment of special groups such as adolescents and the elderly. The second part discusses the different surgical techniques, approaches and comparative results, short- and long-term complications, the repercussions of weight loss on comorbidities, and the criteria for assessing the effectiveness of surgery. The third part discusses postsurgical follow-up, dietary control in the early and subsequent stages after surgery and the schedule for medical and laboratory follow-up, together with the different macro- and micronutrient supplements that should be used depending on the surgical technique employed. A final section is included on pregnancy and bariatric surgery, as well as tables and figures that complement the text. Although bariatric surgery continues to be a questionable treatment for obesity, the results correcting excess weight, with improvements in associated comorbidities and in quality of life, confirm that this option could be the treatment of choice in selected patients when the appropriate surgical technique and correct preand postoperative follow-up are employed

    Clonal chromosomal mosaicism and loss of chromosome Y in elderly men increase vulnerability for SARS-CoV-2

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    The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) had an estimated overall case fatality ratio of 1.38% (pre-vaccination), being 53% higher in males and increasing exponentially with age. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, we found 133 cases (1.42%) with detectable clonal mosaicism for chromosome alterations (mCA) and 226 males (5.08%) with acquired loss of chromosome Y (LOY). Individuals with clonal mosaic events (mCA and/or LOY) showed a 54% increase in the risk of COVID-19 lethality. LOY is associated with transcriptomic biomarkers of immune dysfunction, pro-coagulation activity and cardiovascular risk. Interferon-induced genes involved in the initial immune response to SARS-CoV-2 are also down-regulated in LOY. Thus, mCA and LOY underlie at least part of the sex-biased severity and mortality of COVID-19 in aging patients. Given its potential therapeutic and prognostic relevance, evaluation of clonal mosaicism should be implemented as biomarker of COVID-19 severity in elderly people. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, individuals with clonal mosaic events (clonal mosaicism for chromosome alterations and/or loss of chromosome Y) showed an increased risk of COVID-19 lethality

    Worldwide trends in underweight and obesity from 1990 to 2022: a pooled analysis of 3663 population-representative studies with 222 million children, adolescents, and adults

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    Background Underweight and obesity are associated with adverse health outcomes throughout the life course. We estimated the individual and combined prevalence of underweight or thinness and obesity, and their changes, from 1990 to 2022 for adults and school-aged children and adolescents in 200 countries and territories. Methods We used data from 3663 population-based studies with 222 million participants that measured height and weight in representative samples of the general population. We used a Bayesian hierarchical model to estimate trends in the prevalence of different BMI categories, separately for adults (age ≥20 years) and school-aged children and adolescents (age 5–19 years), from 1990 to 2022 for 200 countries and territories. For adults, we report the individual and combined prevalence of underweight (BMI <18·5 kg/m2) and obesity (BMI ≥30 kg/m2). For schoolaged children and adolescents, we report thinness (BMI <2 SD below the median of the WHO growth reference) and obesity (BMI >2 SD above the median). Findings From 1990 to 2022, the combined prevalence of underweight and obesity in adults decreased in 11 countries (6%) for women and 17 (9%) for men with a posterior probability of at least 0·80 that the observed changes were true decreases. The combined prevalence increased in 162 countries (81%) for women and 140 countries (70%) for men with a posterior probability of at least 0·80. In 2022, the combined prevalence of underweight and obesity was highest in island nations in the Caribbean and Polynesia and Micronesia, and countries in the Middle East and north Africa. Obesity prevalence was higher than underweight with posterior probability of at least 0·80 in 177 countries (89%) for women and 145 (73%) for men in 2022, whereas the converse was true in 16 countries (8%) for women, and 39 (20%) for men. From 1990 to 2022, the combined prevalence of thinness and obesity decreased among girls in five countries (3%) and among boys in 15 countries (8%) with a posterior probability of at least 0·80, and increased among girls in 140 countries (70%) and boys in 137 countries (69%) with a posterior probability of at least 0·80. The countries with highest combined prevalence of thinness and obesity in school-aged children and adolescents in 2022 were in Polynesia and Micronesia and the Caribbean for both sexes, and Chile and Qatar for boys. Combined prevalence was also high in some countries in south Asia, such as India and Pakistan, where thinness remained prevalent despite having declined. In 2022, obesity in school-aged children and adolescents was more prevalent than thinness with a posterior probability of at least 0·80 among girls in 133 countries (67%) and boys in 125 countries (63%), whereas the converse was true in 35 countries (18%) and 42 countries (21%), respectively. In almost all countries for both adults and school-aged children and adolescents, the increases in double burden were driven by increases in obesity, and decreases in double burden by declining underweight or thinness. Interpretation The combined burden of underweight and obesity has increased in most countries, driven by an increase in obesity, while underweight and thinness remain prevalent in south Asia and parts of Africa. A healthy nutrition transition that enhances access to nutritious foods is needed to address the remaining burden of underweight while curbing and reversing the increase in obesit
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