Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear un derstanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5–7 vast areas of the tropics remain understudied.8–11 In the American tropics, Amazonia stands out as the world’s most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepre sented in biodiversity databases.13–15 To worsen this situation, human-induced modifications16,17 may elim inate pieces of the Amazon’s biodiversity puzzle before we can use them to understand how ecological com munities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple or ganism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region’s vulnerability to environmental change. 15%–18% of the most ne glected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lostinfo:eu-repo/semantics/publishedVersio

Tuberculose pulmonar: perfil epidemiológico do sertão Pernambucano, Brasil / Pulmonary tuberculosis: epidemiological profile of sertão Pernambucano, Brazil

Atualmente, observa-se que a tuberculose pulmonar constitui um importante problema de Saúde Pública no mundo, uma vez que esse agravo apresentou, em 2015, 10,4 milhões de casos, dos quais, mais de um milhão de pessoas vieram a óbito. Sob essa perspectiva, o presente artigo tem como objetivo traçar um perfil epidemiológico dos casos de Tuberculose Pulmonar notificados no município de Serra Talhada, entre os anos de 2007 a 2017. Foi realizado um estudo de série histórica observacional do tipo transversal, no intervalo de tempo de 2007 a 2017.  No período investigado o número de casos de tuberculose pulmonar foi de 246 casos, o local que teve a maior prevalência foi Serra Talhada, 287 por 100 mil habitantes. Diante dos dados apresentados, é imprescindível concluir, portanto, que esse estudo corrobora o perfil epidemiológico brasileiro para a Tuberculose Pulmonar, o qual indica variabilidade nos índices de acometimento durante o período analisado

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear understanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5,6,7 vast areas of the tropics remain understudied.8,9,10,11 In the American tropics, Amazonia stands out as the world's most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepresented in biodiversity databases.13,14,15 To worsen this situation, human-induced modifications16,17 may eliminate pieces of the Amazon's biodiversity puzzle before we can use them to understand how ecological communities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple organism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region's vulnerability to environmental change. 15%–18% of the most neglected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lost

The Genome of Anopheles darlingi, the main neotropical malaria vector

Anopheles darlingi is the principal neotropical malaria vector, responsible for more than a million cases of malaria per year on the American continent. Anopheles darlingi diverged from the African and Asian malaria vectors ∼100 million years ago (mya) and successfully adapted to the New World environment. Here we present an annotated reference A. darlingi genome, sequenced from a wild population of males and females collected in the Brazilian Amazon. A total of 10 481 predicted protein-coding genes were annotated, 72% of which have their closest counterpart in Anopheles gambiae and 21% have highest similarity with other mosquito species. In spite of a long period of divergent evolution, conserved gene synteny was observed between A. darlingi and A. gambiae. More than 10 million single nucleotide polymorphisms and short indels with potential use as genetic markers were identified. Transposable elements correspond to 2.3% of the A. darlingi genome. Genes associated with hematophagy, immunity and insecticide resistance, directly involved in vectorhuman and vectorparasite interactions, were identified and discussed. This study represents the first effort to sequence the genome of a neotropical malaria vector, and opens a new window through which we can contemplate the evolutionary history of anopheline mosquitoes. It also provides valuable information that may lead to novel strategies to reduce malaria transmission on the South American continent. The A. darlingi genome is accessible at www.labinfo.lncc.br/index.php/anopheles- darlingi. © 2013 The Author(s)

ATLANTIC EPIPHYTES: a data set of vascular and non-vascular epiphyte plants and lichens from the Atlantic Forest

Epiphytes are hyper-diverse and one of the frequently undervalued life forms in plant surveys and biodiversity inventories. Epiphytes of the Atlantic Forest, one of the most endangered ecosystems in the world, have high endemism and radiated recently in the Pliocene. We aimed to (1) compile an extensive Atlantic Forest data set on vascular, non-vascular plants (including hemiepiphytes), and lichen epiphyte species occurrence and abundance; (2) describe the epiphyte distribution in the Atlantic Forest, in order to indicate future sampling efforts. Our work presents the first epiphyte data set with information on abundance and occurrence of epiphyte phorophyte species. All data compiled here come from three main sources provided by the authors: published sources (comprising peer-reviewed articles, books, and theses), unpublished data, and herbarium data. We compiled a data set composed of 2,095 species, from 89,270 holo/hemiepiphyte records, in the Atlantic Forest of Brazil, Argentina, Paraguay, and Uruguay, recorded from 1824 to early 2018. Most of the records were from qualitative data (occurrence only, 88%), well distributed throughout the Atlantic Forest. For quantitative records, the most common sampling method was individual trees (71%), followed by plot sampling (19%), and transect sampling (10%). Angiosperms (81%) were the most frequently registered group, and Bromeliaceae and Orchidaceae were the families with the greatest number of records (27,272 and 21,945, respectively). Ferns and Lycophytes presented fewer records than Angiosperms, and Polypodiaceae were the most recorded family, and more concentrated in the Southern and Southeastern regions. Data on non-vascular plants and lichens were scarce, with a few disjunct records concentrated in the Northeastern region of the Atlantic Forest. For all non-vascular plant records, Lejeuneaceae, a family of liverworts, was the most recorded family. We hope that our effort to organize scattered epiphyte data help advance the knowledge of epiphyte ecology, as well as our understanding of macroecological and biogeographical patterns in the Atlantic Forest. No copyright restrictions are associated with the data set. Please cite this Ecology Data Paper if the data are used in publication and teaching events. © 2019 The Authors. Ecology © 2019 The Ecological Society of Americ

Estudo da susceptibilidade à infecção pelo HIV-1 e da progressão da AIDS em associação ao polimorfismo no gene Mbl (Lectina Ligadora de Manose)

The low serum concentration of Mannose-Binding Lectin (MBL) is associated to the presence of variant alleles Mbl-*B, Mbl-*C and Mbl-*D, and it results in an increased susceptibility to recurrent infections. The present study investigated the association between the Mbl gene polymorphism and the susceptibility to HIV-1 infection. A fragment of 349 bp from the exon 1 of the Mbl gene was amplified by PCR and then submitted to RFLP analysis using the endonucleases BanI and MboII, aiming the identification of the variant alleles. The study of 145 seropositive patients and 99 healthy controls showed the presence of alleles Mbl-*A, Mbl-*B and Mbl-*D, with frequencies of 69%, 22% and 9% among patients and 70.2%, 13.6% and 16.2% among healthy controls, respectively. The analysis of the genotype frequencies showed a high prevalence of the genotypes carriers of variant Mbl-*B among patients seropositive as compared to the healthy controls. Furthermore, the genotype B/B was six times more frequent among patients than the observed to the healthy controls (χ2=4.042; p=0.044). The mean viral load was lower in HIV-1 seropositive patient carrying the Mbl-*A allele than those carrying the variant Mbl-*B allele (5,821 copies/mL vs. 52,253 copies/mL; p= 0.05). Furthermore, patients carrying the allele Mbl-*A showed a significant reduction of the viral load (p<0.001), that was not observed among those carrying the variant Mbl-*B (p=0.999). The results suggest the importance of the Mbl gene polymorphism on the clinical evolution of the patients infected by HIV-1 and that the identification of the Mbl genetic profile, among HIV-1 infected patients, may be an important tool to monitor the evolution and the prognosis of diseases.CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível SuperiorAs baixas concentrações séricas de Lecitina Ligante de Manose (MBL) estão associadas com a presença das variantes alélicas Mbl-*B, Mbl-*C e Mbl-*D, e resultam em um aumento na susceptibilidade a infecções recorrentes. No presente estudo foi investigada a associação entre o polimorfismo no gene Mbl e a susceptibilidade à infecção pelo HIV-1. Um fragmento de 349 pb do exon 1 do gene Mbl foi amplificado por PCR e, posteriormente, submetido à análise de restrição com as endonucleases BanI e MboII, para a identificação dos alelos. A avaliação de 145 pacientes soropositivos e de 99 controles mostrou a presença dos alelos Mbl-*A, Mbl-*B e Mbl-*D, cujas freqüências foram de 69%, 22% e 9% no grupo de pacientes e de 70,2%, 13,6% e 16,2% entre os controles. A análise das freqüências genotípicas mostrou uma maior prevalência dos genótipos com a variante alélica Mbl-*B entre os pacientes soropositivos quando comparadas à do grupo controle. Ademais, o genótipo B/B foi seis vezes mais freqüente no grupo de pacientes infectados (χ2=4,042; p=0,044). A média da carga viral plasmática foi menor nos pacientes HIV-1 soropositivos, portadores do alelo Mbl-*A, quando comparado aos pacientes soropositivos apresentando a variante alélica Mbl-*B (5.821 cópias/mL x 52.253 cópias/mL; p= 0,05). Ademais os pacientes portadores do alelo Mbl-*A apresentaram uma significativa redução da viremia plasmática (p<0,001), o que não foi observado para os portadores da variante Mbl-*B (p=0,999). Esses resultados sugerem a importância do polimorfismo no gene Mbl na evolução clínica do paciente infectado pelo HIV-1 e que a identificação do perfil genético do gene Mbl, em portadores da infecção pelo HIV-1, pode ser importante na avaliação da evolução e do prognóstico da doença

Caracterização genotípica do Vírus Varicela-Zoster em casos de varicela e Herpes zoster em Belém-Pará, Brasil

Varicella zoster virus (VZV) can cause chickenpox during primary infection, subsequently establishing a latent infection. In case of reactivation of the virus, the herpes zoster may occur. Analysis of the presence of IgG and IgM is critical to determine the prevalence of this virus in the Metropolitan Region of Belém. The study of specific nucleotide polymorphisms is used to define the genotypes of VZV. Analysis of ORFs 22, 38 and 54 identified genotypes of VZV according to the classification established in conference July 25, 2008 in Whitechapel, London / UK, where the strains of VZV detected and characterized by sequencing of SNPs were grouped into classes 1 through 5. To evaluate the prevalence of antibodies and describe the circulating genotypes was the aim of this study. The frequency of IgM and IgG antibodies in cases of chickenpox was 68.2% and 48.2%, respectively. Cases of herpes zoster showed prevalence of anti-VZV IgG and IgM of 87.5% and 12.5%, respectively. The genotypes 1 or 3 and 5 were present in 13 samples sequenced, and the European strain (class 1 or 3) was found in samples from all the cities studied. The identification of strains circulating VZV is extremely important because of the association of specific genotypes with clinical harshest and to assess the implementation of the vaccine in the National Immunization Program.CNPq - Conselho Nacional de Desenvolvimento Científico e TecnológicoO vírus Varicela-zoster (VVZ) pode causar varicela durante a infecção primária, estabelecendo posteriormente uma infecção latente. Na ocorrência de reativação do vírus, pode surgir o herpes zoster. A análise da presença de anticorpos IgG e IgM é fundamental para verificar a prevalência deste vírus na Região Metropolitana de Belém. O estudo de polimorfismos nucleotídicos específicos é utilizado para definir os genótipos do VVZ. A análise das ORFs 22, 38 e 54 permitiu identificar os genótipos do VVZ de acordo com a classificação estabelecida na conferência de 25 de julho de 2008 em Whitechapel, Londres/Reino Unido, em que as cepas de VVZ detectadas e caracterizadas por sequenciamento dos SNPs foram agrupadas em classes de 1 a 5. Avaliar a prevalência de anticorpos e descrever os genótipos circulantes foi o objetivo deste estudo. A frequência de anticorpos IgG e IgM nos casos de varicela foi 68,2% e 48,2%, respectivamente. Os casos de herpes zoster apresentaram prevalência de anti- VVZ IgG e IgM de 87,5% e 12,5%, respectivamente. Os genótipos 1 ou 3 e 5 estavam presentes nas 13 amostras sequenciadas, sendo que a cepa Européia (classe 1 ou 3) foi encontrada em amostras de todos os municípios estudados. A identificação das cepas VVZ circulantes é de extrema importância em virtude da associação de determinados genótipos a quadros clínicos mais severos e para avaliar a implantação da vacina no Programa Nacional de Imunização

Hodgkin lymphoma: epidemiológical aspects and subtypes diagnosed in a reference hospital in Pará State, Brazil

Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Hospital Ophir Loyola. Departamento de Patologia. Belém, Pará, Brasil.Centro Universitário do Estado do Pará. Belém, Pará, Brasil.Universidade Federal do Pará. Núcleo de Medicina Tropical. Belém, Pará, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Os linfomas são neoplasias do sistema imunitário com origem em linfócitos B, T ou células natural killer que envolvem os tecidos linfoides que estão associados ao crescimento de massas tumorais. O linfoma de Hodgkin (LH) é uma neoplasia linfoproliferativa caracterizada histopatologicamente pela presença de células neoplásicas com variada morfologia denominadas Reed-Sternberg. O objetivo deste trabalho foi descrever o perfil epidemiológico e subtipos dos LH diagnosticados no período de 1996 a 2005 no Hospital Ophir Loyola em Belém, Estado do Pará, Brasil. Do total, 64,6 % (42/65) dos pacientes com LH eram do sexo masculino e 35,4 % (23/65) do feminino com faixa etária variando entre 2 e 84 anos. Os subtipos de LH registraram taxas de 50,8 % (33/65), 26,2% (17/65), 15,4% (10/65) e 7,6% (5/65) para esclerose nodular, celularidade mista, depleção linfocitária e predominância linfocitária, respectivamente. Os LH, na década do estudo (1996-2005), foram mais expressivos na faixa infanto-juvenil, na qual prevaleceu o subtipo esclerose nodular nas amostras diagnosticadas no Estado do Pará.Lymphomas are neoplasias of the immune system originating from B and T cells or natural killer cells which involve lymphoid tissues that are associated with the growth of tumor masses. Hodgkin's lymphoma (HL) is a lymphoproliferative malignancy characterized pathologically by the presence of neoplastic cells with a different morphology called Reed-Sternberg. The aim of this study was to describe the epidemiological profile and subtypes of HL diagnosed from 1996 to 2005 at Ophir Loyola Hospital in Belém, Pará State, Brazil. Of the total, 64.6% (42/65) of patients with HL were male and 35.4 % (23/65) of women with ages ranging from 2 to 84 years old. HL subtypes reported rates of 50.8 % (33/65), 26.2% (17/65), 15.4 % (10/65) and 7.6% (5/65) to nodular sclerosis, mixed cellularity, lymphocyte depletion and lymphocyte predominance, respectively. HL, in the period of the current study (1996-2005), it was more expressive in groups of children and teenagers which prevailed the nodular sclerosis subtype in samples diagnosed in the Pará State

Varicella-zoster virus: identification of genotypes in cases of varicella and herpes zoster in the Municipalities of Ananindeua, Belém and Marituba, Pará State, Brazil

Universidade Federal do Pará. Núcleo de Medicina Tropical. Belém, PA, Brasil / Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Universidade Federal do Pará. Núcleo de Medicina Tropical. Belém, PA, Brasil / Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Universidade Federal do Pará. Núcleo de Medicina Tropical. Belém, PA, Brasil / Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Este é um estudo do tipo transversal, em que o critério clínico para inclusão das amostras foi a suspeita clínica e/ou aparecimento dos sintomas da varicela ou herpes-zoster para identificação dos genótipos do vírus da varicela-zoster (VVZ), por meio das técnicas de reação em cadeia da polimerase (PCR) e sequenciamento, com posterior pesquisa de polimorfismo de nucleotídeo único (SNP). De novembro de 2008 a março de 2012, foram coletadas 93 amostras (85 casos de varicela e oito de herpes-zoster) de swab nasal, oral e de secreção de vesículas rompidas em vários sítios anatômicos (49 de indivíduos do sexo masculino e 44 do feminino). As estirpes Dumas e Oka parental foram incluídas como referência padrão dos genótipos europeu (classe 1 ou 3) e japonês (classe 2), respectivamente. Estirpes com variabilidade no SNP foram classificadas dentro de um grupo de genótipo denominado mosaico (classe 5). As classes 1 ou 3 foram identificadas em 11 amostras do VVZ, nove casos de varicela e dois casos de herpes-zoster, enquanto que duas amostras apresentaram o genótipo de classe 5, ambos casos de varicela. O genótipo classe 1 ou 3 foi encontrado nos Municípios de Ananindeua, Belém e Marituba, Estado do Pará, Brasil, sendo que o genótipo classe 5 apenas em Ananindeua. A PCR foi sensível em 13 amostras de material direto de vesículas, enquanto que em amostras de saliva não se obteve sucesso.This is a cross-sectional study in which the clinical criteria for inclusion of the samples was the clinical suspicion and/or onset of symptoms of chickenpox or shingles in order to genotype varicella-zoster virus (VZV) by the polymerase chain reaction (PCR) and sequencing techniques, with a search of single nucleotide polymorphisms (SNP) subsequently. From November 2008 to March 2012, 93 samples (85 cases of varicella and eight herpes zoster) were collected from oral, nasal swab and secretion of ruptured vesicles in several anatomical sites (49 male and 44 female). Dumas and Oka parental strains were included as European genotypes of the reference standard (class 1 or 3) and Japanese (class 2) genotypes, respectively. Strains with the SNP variability were classified into a group of genotype describe as Mosaic (class 5). Classes 1 or 3 were identified in 11 samples of VZV, nine cases of varicella and two cases of herpes zoster, while two samples showed the class genotype 5, both cases of varicella. The genotype class 1 or 3 was found in the Municipalities of Ananindeua, Belém and Marituba, Pará State, Brazil, and genotype class 5 only in Ananindeua. PCR was sensitive in just 13 samples of direct vesicles material, but in saliva samples there were not positive results