BACKGROUND Elite controllers (EC) are human immunodeficiency virus (HIV)-positive individuals who can maintain low viral loads for extended periods without antiretroviral therapy due to multifactorial and individual characteristics. Most have a small HIV-1 reservoir composed of identical proviral sequences maintained by clonal expansion of infected CD4+ T cells. However, some have a more diverse peripheral blood mononuclear cell (PBMC)-associated HIV-1 reservoir with unique sequences. OBJECTIVES To understand the turnover dynamics of the PBMC-associated viral quasispecies in ECs with relatively diverse circulating proviral reservoirs. METHODS We performed single genome amplification of the env gene at three time points during six years in two EC with high intra-host HIV DNA diversity. FINDINGS Both EC displayed quite diverse PBMCs-associated viral quasispecies (mean env diversity = 1.9-4.1%) across all time-points comprising both identical proviruses that are probably clonally expanded and unique proviruses with evidence of ongoing evolution. HIV-1 env glycosylation pattern suggests that ancestral and evolving proviruses may display different phenotypes of resistance to broadly neutralising antibodies consistent with persistent immune pressure. Evolving viruses may progressively replace the ancestral ones or may remain as minor variants in the circulating proviral population. MAIN CONCLUSIONS These findings support that the high intra-host HIV-1 diversity of some EC resulted from long-term persistence of archival proviruses combined with the continuous reservoir’s reseeding and low, but measurable, viral evolution despite undetectable viremia.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rapidly spread around the world during 2020, but the precise time in which the virus began to spread locally is difficult to trace for most countries. Here, we estimate the probable onset date of the community spread of SARS-CoV-2 for heavily affected countries from Western Europe and the Americas on the basis of the cumulative number of deaths reported during the early stage of the epidemic. Our results support that SARS-CoV-2 probably started to spread locally in all western countries analysed between mid-January and mid-February 2020, thus long before community transmission was officially recognised and control measures were implemented.

Phylogenetic analyses were crucial to elucidate the origin and spread of the pandemic human immunodeficiency virus type 1 (HIV-1) group M virus, both during the pre-epidemic period of cryptic dissemination in human populations as well as during the epidemic phase of spread. The use of phylogenetics and phylodynamics approaches has provided important insights to track the founder events that resulted in the spread of HIV-1 strains across vast geographic areas, specific countries and within geographically restricted communities. In the recent years, the use of phylogenetic analysis combined with the huge availability of HIV sequences has become an increasingly important approach to reconstruct HIV transmission networks and understand transmission dynamics in concentrated and generalised epidemics. Significant efforts to obtain viral sequences from newly HIV-infected individuals could certainly contribute to detect rapidly expanding HIV-1 lineages, identify key populations at high-risk and understand what public health interventions should be prioritised in different scenarios.

Abstract Background and Aims Shrubs are an important floristic element of tropical forests; however, research on plants with this growth form is still scarce. the main objective of this study was to analyze the influence of elevation and disturbance on shrub richness and distribution patterns in the central region of Veracruz, Mexico. Methods An elevational gradient (20-3500 m a.s.l.) was established along the eastern slopes of the Cofre de Perote, where floristic sampling was conducted at eight study sites within elevational belts of approximately 500 m each. We recorded the abundance of shrubs within 120 plots of 20 × 20 m, distributed in three habitats: conserved, disturbed and secondary forest. the species richness and floristic composition were analyzed, and the resulting data were compared between the different elevational belts and degrees of forest disturbance. Key results We recorded 118 species and 14 morphospecies of shrubs, representing 8.6% of the shrubs reported for Veracruz. the forest fragments at elevations of 500 and 1000 m are the most species-rich; however, these are the most susceptible to human activities. the anthropogenic disturbance of these forests can increase species richness locally, but at the same time modifies the floristic composition from a conserved habitat to a secondary one. Conclusions The present study is the first in the Neotropics that considers and analyzes shrubs as an individual group along a complete gradient using a uniform and comparable sampling method. this enabled us to detect which fragments of conserved, disturbed or secondary forest are highly diverse and at the same time susceptible to human disturbance. these sites can serve as strategic buffer zones and refuge of this group of plants, since regardless of their use intensity, they could and should be considered in future conservation plans in this region threatened by environmental degradation.

Resumen Antecedentes y Objetivos Los arbustos son un elemento florístico importante de los bosques tropicales; sin embargo, la investigación sobre plantas con esta forma de crecimiento aún es escasa. El objetivo principal de este estudio consistió en analizar la influencia de la elevación y la perturbación en los patrones de distribución y diversidad de los arbustos en la región central de Veracruz, México. Métodos Se estableció un gradiente elevacional (20-3500 m s.n.m) en la ladera este del Cofre de Perote, donde se realizó un muestreo florístico en ocho pisos elevacionales separados por 500 m cada uno. Registramos la abundancia de arbustos dentro de 120 parcelas de 20 × 20 m, distribuidas en tres hábitats: bosque conservado, perturbado y secundario. Se analizó la riqueza, diversidad y composición florística; además, se compararon los datos resultantes entre los diferentes pisos elevacionales y los grados de perturbación del bosque. Resultados clave Se registraron 118 especies y 14 morfoespecies de arbustos, lo que representa 8.6% de los reportados para Veracruz. Los fragmentos de bosque en las elevaciones de 500 y 1000 m son los más ricos en número de especies, pero también son los más susceptibles a las perturbaciones humanas. La influencia antrópica sobre estos bosques puede incrementar la diversidad de especies a nivel local, pero al mismo tiempo modifica la composición florística de un hábitat conservado a uno secundario. Conclusiones El presente estudio es el primero en el Neotrópico en considerar y analizar los arbustos como un grupo individual a lo largo de un gradiente completo utilizando un método de muestreo uniforme y comparable. Esto permitió detectar aquellos fragmentos de bosque conservado, perturbado o secundario que son altamente diversos y susceptibles a los distrubios antrópicos. Estos sitios sirven como zonas estratégicas de amortiguación y refugio de este grupo de plantas, ya que independientemente de la intensidad de su uso, estos podrían y deberían considerarse en futuros planes de conservación en esta región amenazada por la degradación ambiental.

BACKGROUND In Brazil, the Yellow Fever virus (YFV) is endemic in the Amazon, from where it eventually expands into epidemic waves. Coastal south-eastern (SE) Brazil, which has been a YFV-free region for eight decades, has reported a severe sylvatic outbreak since 2016. The virus spread from the north toward the south of the Rio de Janeiro (RJ) state, causing 307 human cases with 105 deaths during the 2016-2017 and 2017-2018 transmission seasons. It is unclear, however, whether the YFV would persist in the coastal Atlantic Forest of RJ during subsequent transmission seasons. OBJECTIVES To conduct a real-time surveillance and assess the potential persistence of YFV in the coastal Atlantic Forest of RJ during the 2018-2019 transmission season. METHODS We combined epizootic surveillance with fast diagnostic and molecular, phylogenetic, and evolutionary analyses. FINDINGS Using this integrative strategy, we detected the first evidence of YFV re-emergence in the third transmission season (2018-2019) in a dying howler monkey from the central region of the RJ state. The YFV detected in 2019 has the molecular signature associated with the current SE YFV outbreak and exhibited a close phylogenetic relationship with the YFV lineage that circulated in the same Atlantic Forest fragment during the past seasons. This lineage circulated along the coastal side of the Serra do Mar mountain chain, and its evolution seems to be mainly driven by genetic drift. The potential bridge vector Aedes albopictus was found probing on the recently dead howler monkey in the forest edge, very close to urban areas. MAIN CONCLUSIONS Collectively, our data revealed that YFV transmission persisted at the same Atlantic Forest area for at least three consecutive transmission seasons without the need of new introductions. Our real-time surveillance strategy permitted health authorities to take preventive actions within 48 h after the detection of the sick non-human primate. The local virus persistence and the proximity of the epizootic forest to urban areas reinforces the concern with regards to the risk of re-urbanisation and seasonal re-emergence of YFV, stressing the need for continuous effective surveillance and high vaccination coverage in the SE region, particularly in RJ, an important tourist location.

A recent study showed that infectivity of Zika virus (ZIKV) Asian genotype was enhanced by an alanine-to-valine amino acid substitution at residue 188 of the NS1 protein, but the precise time and location of origin of this mutation were not formally estimated. Here, we applied a Bayesian coalescent-based framework to estimate the age and location of the ancestral viral strain carrying the A188V substitution. Our results support that the ancestral ZIKV strain carrying the A188V substitution arose in Southeastern Asia at the early 2000s and circulated in that region for some time (5-10 years) before being disseminated to Southern Pacific islands and the Americas.

Abstract: Background and Aims: The revision of herbarium specimens of Hoffmannia (Rubiaceae) and the extensive exploration by the authors has resulted in the discovery of new species within this genus. Hoffmannia uxpanapense Cast.-Campos and Bautista-Bello is described and illustrated as a new species of the Rubiaceae family from southern Mexico, collected in the evergreen tropical forest of Uxpanapa in Veracruz and Oaxaca. Methods: The specimens of the genus Hoffmannia of the state of Veracruz were studied, a matrix of morphological data was elaborated, and a cluster analysis was carried out to differentiate the species and to detect their similarities. Key results: The specimens identified as “H. wendtii” presented different morphological characters to the species already described in this genus. As this name has not been published, it was considered as a new species that still needs to be formally described. This species shows similarities with H. cuneatissima, H. minuticarpa and H. arqueonervosa. Nevertheless, H. uxpanapense differs by being a climbing shrub, with larger internodes on the stem, larger inflorescences and a greater number of white flowers per inflorescence. Conclusions: Hoffmannia uxpanapense belongs to a group of endemic species of Mexico (H. cuneatissima, H. minuticarpa and H. arqueonervosa), and this new taxon is considered as endemic of the southern zone of Veracruz and Oaxaca.

Resumen: Antecedentes y Objetivos: La revisión de especímenes de herbario de Hoffmannia (Rubiaceae) y las intensivas exploraciones por los autores originaron el descubrimiento de nuevas especies de este género. Se describe e ilustra a Hoffmannia uxpanapense Cast.-Campos y Bautista-Bello como una nueva especie del sur de México, colectada en la selva alta perennifolia de Uxpanapa en Veracruz y Oaxaca. Métodos: Se revisaron los ejemplares del género Hoffmannia para el estado de Veracruz, se elaboró una matriz de datos morfológicos y se llevó a cabo un análisis de conglomerados para diferenciar a las especies y detectar sus similitudes. Resultados clave: Los ejemplares identificados como “H. wendtii” presentaron caracteres morfológicos diferentes a las especies ya descritas en este género. Dado que este nombre no ha sido publicado, se consideró como una especie nueva aún por describir formalmente. Este taxon muestra similitudes con H. cuneatissima, H. minuticarpa y H. arqueonervosa. Sin embargo, H. uxpanapense difiere por ser un arbusto trepador, con entrenudos del tallo más largos, inflorescencias más grandes y un mayor número de flores de color blanco por inflorescencia. Conclusiones: Hoffmannia uxpanapense se integra a un grupo de especies endémicas de México (H. cuneatissima, H. minuticarpa y H. arqueonervosa), y se considera a este nuevo taxon como endémico de la zona sur de Veracruz y Oaxaca.

Particle Swarm Optimization (PSO) is a non-direct search method for numerical optimization. The key advantages of this metaheuristic are principally associated to its simplicity, few parameters and high convergence rate. In the canonical PSO using a fully connected topology, a particle adjusts its position by using two attractors: the best record stored for the current agent, and the best point discovered for the entire swarm. It leads to a high convergence rate, but also progressively deteriorates the swarm diversity. As a result, the particle swarm frequently gets attracted by sub-optimal points. Once the particles have been attracted to a local optimum, they continue the search process within a small region of the solution space, thus reducing the algorithm exploration. To deal with this issue, this paper presents a variant of the Random Sampling in Variable Neighborhoods (RSVN) procedure using a Lévy distribution, which is able to notably improve the PSO search ability in multimodal problems.

Particle Swarm Optimization (PSO) es un método de búsqueda no directo para la optimización numérica. Las principales ventajas de esta meta-heurística están relacionadas principalmente con su simplicidad, pocos parámetros y alta tasa de convergencia. En el PSO canónico usando una topología totalmente conectada, una partícula ajusta su posición usando dos atractores: el mejor registro almacenado por el individuo y el mejor punto descubierto por la bandada completa. Este esquema conduce a un alto factor de convergencia, pero también deteriora la diversidad de la población progresivamente. Como resultado la bandada de partículas frecuentemente es atraída por puntos sub-óptimos. Una vez que las partículas han sido atraídas hacia un óptimo local, ellas continúan el proceso de búsqueda dentro de una región muy pequeña del espacio de soluciones, reduciendo las capacidades de exploración del algoritmo. Para tratar esta situación este artículo presenta una variante del procedimiento Random Sampling in Variable Neighborhoods (RSVN) usando una distribución de Lévy. Este algoritmo es capaz de mejorar notablemente la capacidad de búsqueda de los algoritmos PSO en problemas multimodales de optimización.

Hoffmannia rzedowskiana Cast.-Campos, Bautista-Bello and Lorence (Rubiaceae) is described and illustrated as a new species from southern Mexico (Chiapas, Oaxaca and Veracruz) and Nicaragua. In Veracruz, it occurs in the region of Los Tuxtlas and Uxpanapa near the border with the Chimalapas (Oaxaca). This species is related to Hoffmannia discolor, from which it differs by presenting leaves which are pilose on the abaxial surface, sessile to shortly petiolate, lateral veins 19-23(-26) pairs, pubescent flowers and a linear stigma.

Se describe e ilustra a Hoffmannia rzedowskiana Cast.-Campos, Bautista-Bello y Lorence perteneciente a la familia Rubiaceae como una nueva especie del sur de México (Chiapas, Oaxaca y Veracruz) y Nicaragua. En Veracruz se ha registrado en la región de Los Tuxtlas y en Uxpanapa cerca de los límites con los Chimalapas (Oaxaca). Esta especie muestra similitudes con Hoffmannia discolor, de la que difiere por presentar hojas pilosas por el envés, sésiles a cortamente pecioladas, nervaduras laterales 19-23(-26) pares, flores pubescentes y estigma linear.

Hoffmannia arqueonervosa Cast.-Campos (Rubiaceaea) is described and illustrated as a new species from the gallery forest in the Center of Veracruz and on the eastern slopes of the Cofre de Perote volcano, Veracruz, Mexico. This species is related to Hoffmannia cuneatissima B. L. Robins.; however, the petioles and internodes of H. arqueonervosa are longer, leaves are glabrous and fruits are larger.

Se describe e ilustra a Hoffmannia arqueonervosa Cast.-Campos perteneciente a la familia Rubiaceae como una nueva especie del centro de Veracruz, en las faldas orientales del volcán Cofre de Perote, Veracruz, México. Esta especie muestra similitudes con Hoffmannia cuneatissima B. L. Robins.; sin embargo, H. arqueonervosa difiere de H. cuneatissima por presentar entrenudos y peciolos más largos, hojas glabras y frutos más grandes.

Particle Swarm Optimization (PSO) is a bioinspired meta-heuristic for solving complex global optimization problems. In standard PSO, the particle swarm frequently gets attracted by suboptimal solutions, causing premature convergence of the algorithm and swarm stagnation. Once the particles have been attracted to a local optimum, they continue the search process within a minuscule region of the solution space, and escaping from this local optimum may be difficult. This paper presents a modified variant of constricted PSO that uses random samples in variable neighborhoods for dispersing the swarm whenever a premature convergence (or stagnation) state is detected, offering an escaping alternative from local optima. The performance of the proposed algorithm is discussed and experimental results show its ability to approximate to the global minimum in each of the nine well-known studied benchmark functions.

All modern society investigates in the field of Travel Behavior because of the significance for all social and economical process of a country. The problems related with travel behavior are not structured; the Artificial Intelligence techniques have a high interest in its solution, specially related with the knowledge representation and the uncertainty. The use of advanced computer techniques like Knowledge Engineering and Cognitive Mapping is also relevant from diverse points of view. A crucial role is played by the process of modeling and defining what will be taken into account in this kind of problems, for that reason in this paper are described some important ideas of how to understand and extract the mental representation of individuals in the decision making and planning of trips, related to daily travels, because this is useful information that can be used in transport demand prediction, analysis and studies.

Circulation of a new dengue virus (DENV)-3 genotype was recently described in Brazil and Colombia, but the precise classification of this genotype has been controversial. Here we perform phylogenetic and nucleotide-distance analyses of the envelope gene, which support the subdivision of DENV-3 strains into five distinct genotypes (GI to GV) and confirm the classification of the new South American genotype as GV. The extremely low genetic distances between Brazilian GV strains and the prototype Philippines/L11423 GV strain isolated in 1956 raise important questions regarding the origin of GV in South America.

We recently performed a molecular epidemiology survey of human immunodeficiency virus type 1 (HIV-1) infection in Miracema, a small city in Southeast Brazil, and found multiple monophyletic clusters, consistent with independent introductions and spread of different viral lineages in the city. Here we apply Bayesian coalescent-based methods to the two largest subtype B clusters and estimate that the most recent common ancestors that gave rise to these two transmission chains were in circulation around 1991-1992. The finding that HIV-1 spread in this Brazilian small city was already taking place at a time Aids was considered a problem restricted to large urban centers may have important public health implications.