Effect of urban vs. rural residence on the association between atopy and wheeze in Latin America: findings from a case-control analysis.

BACKGROUND: The association between atopy and asthma is attenuated in non-affluent populations, an effect that may be explained by childhood infections such as geohelminths. OBJECTIVE: To investigate the association between atopy and wheeze in schoolchildren living in urban and rural areas of Ecuador and examine the effects of geohelminths on this association. METHODS: We performed nested case-control studies among comparable populations of schoolchildren living in rural communities and urban neighbourhoods in the Province of Esmeraldas, Ecuador. We detected geohelminths in stool samples, measured recent wheeze and environmental exposures by parental questionnaire, and atopy by specific IgE (sIgE) and skin prick test (SPT) reactivity to aeroallergens. RESULTS: Atopy, particularly sIgE to house dust mite (HDM), was more strongly associated with recent wheeze in urban than rural schoolchildren: (urban, adj. OR 5.19, 95% CI 3.37-8.00, P < 0.0001; rural, adj. OR 1.81, 95%CI 1.09-2.99, P = 0.02; interaction, P < 0.001). The population fractions of wheeze attributable to atopy were approximately two-fold greater in urban schoolchildren: SPT to any allergen (urban 23.5% vs. rural 10.1%), SPT to HDM (urban 18.5% vs. rural 9.6%), and anti-HDM IgE (urban 26.5% vs. rural 10.5%), while anti-Ascaris IgE was related to wheeze in a high proportion of rural (49.7%) and urban (35.4%) children. The association between atopy and recent wheeze was attenuated by markers of geohelminth infections. CONCLUSIONS: Our data suggest that urban residence modifies the association between HDM atopy and recent wheeze, and this effect is explained partly by geohelminth infections

Obituary: William Mark Whitten (1954−2019)

On April 11, 2019, Dr. William Mark Whitten, a prolific neotropical orchid biologist passed away unexpectedly. He leaves an extensive corpus of work focused on (but not limited to) orchid pollination and systematics, and over four thousand beautifully prepared herbarium specimens. Everyone that met Mark can agree that he was a wonderful human being, kind to everyone, incredibly knowledgeable and yet very humble. Always of a calm demeanor, great sense of humor, and willingness to help, Mark was an outstanding and relatable collaborator, and his publications (more than a hundred; see list below) are evidence of a productive and highly collaborative academic career.UCR::Vicerrectoría de Docencia::Ciencias Básicas::Facultad de Ciencias::Escuela de BiologíaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Agroalimentarias::Jardín Botánico Lankester (JBL

A Natural Language Processing Pipeline to extract phenotypic data from formal taxonomic descriptions with a focus on flagellate plants

Assembling large-scale phenotypic datasets for evolutionary and biodiversity studies of plants can be extremely difficult and time consuming. New semi-automated Natural Language Processing (NLP) pipelines can extract phenotypic data from taxonomic descriptions, and their performance can be enhanced by incorporating information from ontologies, like the Plant Ontology (PO) and the Plant Trait Ontology (TO). These ontologies are powerful tools for comparing phenotypes across taxa for large-scale evolutionary and ecological analyses, but they are largely focused on terms associated with flowering plants. We describe a bottom-up approach to identify terms from flagellate plants (including bryophytes, lycophytes, ferns, and gymnosperms) that can be added to existing plant ontologies. We first parsed a large corpus of electronic taxonomic descriptions using the Explorer of Taxon Concepts tool (http://taxonconceptexplorer.org/) and identified flagellate plant specific terms that were missing from the existing ontologies. We extracted new structure and trait terms, and we are currently incorporating the missing structure terms to the PO and modifying the definitions of existing terms to expand their coverage to flagellate plants. We will incorporate trait terms to the TO in the near future

Generic realignments in Maxillariinae (Orchidaceae)

Un reciente análisis filogenético de cuatro regiones de ADN para ca. 354 especies de la subtribu Maxillariinae indican fuertemente que el género Maxillaria, en su circunscripción tradicional, es altamente polifilético. Presentamos una nueva clasificación filogenética para Maxillariinae que reconoce 17 géneros. Los cambios necesarios incluyen: 1) la resurrección de los géneros Camaridium, Heterotaxis, y Ornithidium; 2) el reconocimiento de los recientes segregados genéricos Brasiliorchis (=Maxillaria sección Repentes), Christensonella (=Maxillaria sección Urceolatae), Nitidobulbon (en prensa), y una Sauvetrea recircunscrita (=Maxillaria sección Trigonae); 3) la adopción de los nuevos géneros Inti (=Maxillaria sección Polyphyllae), Mapinguari, Maxillariella (=Maxillaria secciones Ebulbes y Erectae), y Rhetinantha; 4) transferencias de Maxillaria sección Reflexae a Ornithidium, y Maxillaria sección Rufescens a Mormolyca; y 5) puesta en sinonimia de los géneros Adamanthus, Pseudomaxillaria, Psittacoglossum y Sepalosaccus (bajo Camaridium), Anthosiphon (bajo Cryptocentrum), Chrysocycnis (bajo Mormolyca), Dicrypta, Marsupiaria y Pentulops (bajo Heterotaxis), y Laricorchis, Neo-Urbania, y Siagonanthus (bajo Ornithidium). Algunos sinónimos nuevos al nivel de especie también son presentados.A recent phylogenetic analysis of four DNA regions for ca. 354 species of core Maxillariinae strongly indicate that the genus Maxillaria, as traditionally circumscribed, is grossly polyphyletic. We present a new phylogenetic classification for core Maxillariinae that recognizes 17 genera. Necessary realignments include: 1) resurrection of the genera Camaridium, Heterotaxis, and Ornithidium; 2) recognition of the recent segregates Brasiliorchis (=Maxillaria sect. Repentes), Christensonella (=Maxillaria sect. Urceolatae), Nitidobulbon (in press), and a recircumscribed Sauvetrea (=Maxillaria sect. Trigonae); 3) adoption of the new genera Inti (=Maxillaria sect. Polyphyllae), Mapinguari, Maxillariella (=Maxillaria sections Ebulbes and Erectae), and Rhetinantha; 4) transfers from Maxillaria sect. Reflexae to Ornithidium, and Maxillaria sect. Rufescens to Mormolyca; and 5) synonymizing of the genera Adamanthus, Pseudomaxillaria, Psittacoglossum, and Sepalosaccus (under Camaridium), Anthosiphon (under Cryptocentrum), Chrysocycnis (under Mormolyca), Dicrypta, Marsupiaria, and Pentulops (under Heterotaxis), and Laricorchis, Neo-urbania, and Siagonanthus (under Ornithidium). Some new synonyms at the specific level are also presented.National Science Foundation/[DEB-0234064]/NSF/Estados UnidosFundação de Amparo à Pesquisa do Estado de São Paulo/[01/08958-1]/FAPESP/BrasilConsejo Nacional de Ciencia y Tecnología/[]/CONACYT/MéxicoRoyal Botanic Gardens, Kew/[]//InglaterraAmerican Orchid Society/[]/AOS/Estados UnidosUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Agroalimentarias::Jardín Botánico Lankester (JBL

Patent Human Infections with the Whipworm, Trichuris trichiura, Are Not Associated with Alterations in the Faecal Microbiota

Background: The soil-transmitted helminth (STH), Trichuris trichiura colonises the human large intestine where it may modify inflammatory responses, an effect possibly mediated through alterations in the intestinal microbiota. We hypothesised that patent T. trichiura infections would be associated with altered faecal microbiota and that anthelmintic treatment would induce a microbiota resembling more closely that observed in uninfected individuals. Materials and Methods: School children in Ecuador were screened for STH infections and allocated to 3 groups: uninfected, T. trichiura only, and mixed infections with T. trichiura and Ascaris lumbricoides. A sample of uninfected children and those with T. trichiura infections only were given anthelmintic treatment. Bacterial community profiles in faecal samples were studied by 454 pyrosequencing of 16 S rRNA genes. Results: Microbiota analyses of faeces were done for 97 children: 30 were uninfected, 17 were infected with T. trichiura, and 50 with T. trichiura and A. lumbricoides. Post-treatment samples were analyzed for 14 children initially infected with T. trichiura alone and for 21 uninfected children. Treatment resulted in 100% cure of STH infections. Comparisons of the microbiota at different taxonomic levels showed no statistically significant differences in composition between uninfected children and those with T. trichiura infections. We observed a decreased proportional abundance of a few bacterial genera from the Clostridia class of Firmicutes and a reduced bacterial diversity among children with mixed infections compared to the other two groups, indicating a possible specific effect of A. lumbricoides infection. Anthelmintic treatment of children with T. trichiura did not alter faecal microbiota composition. Discussion: Our data indicate that patent human infections with T. trichiura may have no effect on faecal microbiota but that A. lumbricoides colonisation might be associated with a disturbed microbiota. Our results also catalogue the microbiota of rural Ecuadorians and indicate differences with individuals from more urban industrialised societies

Preliminary molecular phylogenetics of Sobralia and relatives (Orchidaceae: Sobralieae)

With over 200 species, the orchid tribe Sobralieae is a major constituent of the Neotropical flora. As currently circumscribed, the tribe includes four genera: Elleanthus, Epilyna, Sertifera, and Sobralia. Most species of these four genera typically produce long, cane-like stems but differ drastically in flower size and inflorescence structure. DNA sequence data support the monophyly of Elleanthus, Epilyna, and Sertifera but not Sobralia, which is a polyphyletic assemblage traditionally placed together due to relatively large flower size. Details of inflorescence structure provide characters that can easily distinguish the different clades of Sobralia. The misleading characteristic of flower size is probably due to at least several shifts in pollination syndrome within the tribe. With few exceptions, species of Sobralia predominantly offer no reward and are pollinated by bees. Elleanthus and Sertifera are small-flowered and mostly pollinated by hummingbirds with legitimate rewards. Nothing is known of pollination in Epilyna. Understanding the evolution of shifts in pollination syndrome will require more empirical observations of pollination within Sobralieae. In addition, increased taxon sampling and improved phylogenetic resolution are needed before generic realignments are made.Con más de 200 especies, la tribu de orquídeas Sobralieae es un componente importante de la riqueza florística de los neotrópicos. Actualmente esta tribu está constituída por cuatro géneros: Elleanthus, Epilyna, Sertifera, y Sobralia. Las plantas de éstos cuatro géneros generalmente producen tallos largos como cañas, pero difieren en forma drástica en el tamaño de la flor y la estructura de las inflorescencias. Datos de ADN apoyan la monofilia de Elleanthus, Epilyna, y Sertifera, pero no de Sobralia. Sobralia es un ensamblaje polifilético, tradicionalmente circunscrito por el gran tamaño de sus flores. Los detalles de la morfología floral y la posición de la inflorescencia proporcionan caracteres que fácilmente permiten distinguir los diferentes clados de Sobralia. El tamaño de la flor y ciertas otras características superficiales probablemente han sufrido cambios evolutivos en respuesta a cambios en el síndrome de polinización dentro de la tribu. La mayoría de las especies de Sobralia no ofrecen ninguna recompensa y son polinizadas por abejas en busca de néctar. Elleanthus y Sertifera tienen flores pequeñas que aparentemente son polinizadas por colibríes, en estos dos géneros las flores ofrecen néctar. No se conoce nada sobre la polinización de Epilyna. Mas observaciones empíricas de los polinizadores de Sobralieae son necesarias para entender la evolución de los síndromes de polinización, y requerirá un mayor muestreo de especies y una mejor resolución filogenética antes de realizar recircumscripciones genéricas.National Science Foundation/[DEB-234064]/NSF/Estados UnidosUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Agroalimentarias::Jardín Botánico Lankester (JBL

Male fetal loss in the U.S. following the terrorist attacks of September 11, 2001

Background: The secondary sex ratio (i.e., the odds of a male birth) reportedly declines following natural disasters, pollution events, and economic collapse. It remains unclear whether this decline results from an excess of male fetal loss or reduced male conceptions. The literature also does not converge as to whether the terrorist attacks of September 11, 2001 induced "communal bereavement", or the widespread feeling of distress among persons who never met those directly involved in the attacks. We test the communal bereavement hypothesis among gravid women by examining whether male fetal deaths rose above expected levels in the US following September 11, 2001. Methods: We apply interrupted time-series methods to all fetal deaths at or greater than the 20(th) week of gestation in the US from 1996 to 2002. Time-series methods control for trends, seasonality, and other forms of autocorrelation that could induce spurious associations. Results: Results support the hypothesis in that the fetal death sex ratio (i.e., the odds of a male fetal death) increased above its expected value in September 2001. Additional analysis of the secondary sex ratio indirectly supports that the terrorist attacks may have threatened the gestation of male more than female fetuses. Conclusions: Societal responses to events such as September 11, 2001 do not appear confined only to persons who have ever met the deceased. The fetal death sex ratio in the US population may serve as a sentinel indicator of the degree to which pregnant women react to population stressors

Generic realignments in Maxillariinae (Orchidaceae): Corrigenda et adenda

UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Agroalimentarias::Jardín Botánico Lankester (JBL