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

Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009; Cianferoni & Bartolozzi 2016; Amorim et al. 2016). This question was again raised in a letter supported by 35 signatories published in the journal Nature (Pape et al. 2016) on 15 September 2016. On 25 September 2016, the following rebuttal (strictly limited to 300 words as per the editorial rules of Nature) was submitted to Nature, which on 18 October 2016 refused to publish it. As we think this problem is a very important one for zoological taxonomy, this text is published here exactly as submitted to Nature, followed by the list of the 493 taxonomists and collection-based researchers who signed it in the short time span from 20 September to 6 October 2016

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

In Vitro Sensitivity of Paired Leishmania (Viannia) braziliensis Samples Isolated before Meglumine Antimoniate Treatment and after Treatment Failure or Reactivation of Cutaneous Leishmaniasis

Submitted by sandra infurna ([email protected]) on 2016-04-07T12:45:31Z No. of bitstreams: 1 leonor_leon_etal_IOC_2015.pdf: 1268112 bytes, checksum: e5b9b4251ed705cc9ed9fcf5bef93b69 (MD5)Approved for entry into archive by sandra infurna ([email protected]) on 2016-04-07T13:50:06Z (GMT) No. of bitstreams: 1 leonor_leon_etal_IOC_2015.pdf: 1268112 bytes, checksum: e5b9b4251ed705cc9ed9fcf5bef93b69 (MD5)Made available in DSpace on 2016-04-07T13:50:06Z (GMT). No. of bitstreams: 1 leonor_leon_etal_IOC_2015.pdf: 1268112 bytes, checksum: e5b9b4251ed705cc9ed9fcf5bef93b69 (MD5) Previous issue date: 2015Fundação Oswaldo Cruz. Bio-Manguinhos. Núcleo de Biossegurança. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica e Vigilância em Leishmanioses. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica e Vigilância em Leishmanioses. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Laboratório de Bioquímica de Tripanosomatídeos. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Imunoparasitologia. Rio de Janeiro, RJ, Brasil.This study evaluated the in vitro sensitivity of paired Leishmania braziliensis samples isolated from the same patient before pentavalent antimonial treatment (Sample A) and after treatment failure or cutaneous leishmaniasis reactivation (Sample B) in patients undergoing intralesional administration or injections (5 mgS/kg/d) of meglumine antimoniate. Fourteen samples from 7 patients were studied. After 24 h of drug exposure, 50% lethal dose (LD50) values for promastigotes ranged from 0.37 mg/mL to 5.86 mg/mL for samples obtained before treatment (A) and 0.89 mg/mL to 7.80 mg/mL for samples obtained after treatment (B). After 48 h, LD50 values ranged from 0.37 mg/mL to 5.75 mg/mL and 0.70 mg/mL to 7.68 mg/mL for A and B samples, respectively. After 48 h, LD50 values for amastigotes ranged from 11.7 to 44.3 μg/mL for A samples and 13.7 to 52.7 μg/mL for B samples. Of 7 patients, 1 discontinued treatment and 6 were cured after retreatment with amphotericin B (4 cases) or meglumine antimoniate (2 cases). Overall the B samples had higher LD50 values than A samples; however the difference was not significant. These results do not support the hypothesis that low-dose and intralesional treatments induce selection of resistant parasites in vitro and suggest that other factors may influence therapeutic outcome in patients with poor response to initial treatment

Outbreak of canine visceral leishmaniasis in Barra Mansa, State of Rio de Janeiro

Submitted by Rodrigo Senorans ([email protected]) on 2015-05-22T16:42:34Z No. of bitstreams: 1 Outbreak of canine visceral leishmaniasis in Barra Mansa, State of Rio de Janeiro.pdf: 692413 bytes, checksum: d91184a04249d6aa693f1a167841a542 (MD5)Approved for entry into archive by Anderson Silva ([email protected]) on 2015-05-25T11:53:18Z (GMT) No. of bitstreams: 1 Outbreak of canine visceral leishmaniasis in Barra Mansa, State of Rio de Janeiro.pdf: 692413 bytes, checksum: d91184a04249d6aa693f1a167841a542 (MD5)Approved for entry into archive by Anderson Silva ([email protected]) on 2015-05-25T11:53:25Z (GMT) No. of bitstreams: 1 Outbreak of canine visceral leishmaniasis in Barra Mansa, State of Rio de Janeiro.pdf: 692413 bytes, checksum: d91184a04249d6aa693f1a167841a542 (MD5)Made available in DSpace on 2015-05-25T15:45:42Z (GMT). No. of bitstreams: 1 Outbreak of canine visceral leishmaniasis in Barra Mansa, State of Rio de Janeiro.pdf: 692413 bytes, checksum: d91184a04249d6aa693f1a167841a542 (MD5) Previous issue date: 2014Instituto Nacional de Infectologia Evandro Chagas/Fundação Oswaldo Cruz (FIOCRUZ) e Prefeitura Municipal de Barra Mansa.Fundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Vigilância em Leishmanioses. Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica em Dermatozoonoses. Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica em Dermatozoonoses. Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica em Dermatozoonoses. Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Vigilância em Leishmanioses. Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Vigilância em Leishmanioses. Rio de Janeiro, RJ, BrasilIntroduction: In Brazil, visceral leishmaniasis (VL) has spread to various regions. This study reports canine cases of VL in Barra Mansa, where human VL cases were recently reported. Methods: Using the human index case, a canine survey was performed by dual-path platform immunochromatography and enzyme-linked immunosorbent assay. Seropositive animals were euthanized. Cultures were collected to detect Leishmania parasites. Results: Serological tests detected 141 canine VL cases, and Leishmania chagasi were isolated from 82.2% animals. Conclusions: Leishmania chagasi is in circulation in Barra Mansa. This study broadens information on the parasite’s distribution in the State of Rio de Janeiro

Thick smear is a good substitute for the thin smear in parasitological confirmation of canine visceral leishmaniasis

Artigo disponível em acesso aberto em https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4944718/Submitted by Janaína Nascimento ([email protected]) on 2019-02-25T14:48:07Z No. of bitstreams: 1 ve_Mello_Cintia_etal_INI_2106.pdf: 784787 bytes, checksum: a732f926486d890004473a2b06a4750b (MD5)Approved for entry into archive by Janaína Nascimento ([email protected]) on 2019-02-26T14:18:49Z (GMT) No. of bitstreams: 1 ve_Mello_Cintia_etal_INI_2106.pdf: 784787 bytes, checksum: a732f926486d890004473a2b06a4750b (MD5)Made available in DSpace on 2019-02-26T14:18:49Z (GMT). No. of bitstreams: 1 ve_Mello_Cintia_etal_INI_2106.pdf: 784787 bytes, checksum: a732f926486d890004473a2b06a4750b (MD5) Previous issue date: 2016Fundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica e Vigilância em Leishmanioses. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica em Dermatozoonoses em Animais Domésticos. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica em Dermatozoonoses em Animais Domésticos. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica e Vigilância em Leishmanioses. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Epidemiologia Clínica. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica e Vigilância em Leishmanioses. Rio de Janeiro, RJ, Brasil.Although direct examination methods are important for diagnosing leishmaniasis, such methods are often neglected because of their low sensitivity relative to other techniques. Our study aimed to evaluate the performance of bone marrow (BM) thick smears and cytocentrifugation tests as alternatives to direct examination for diagnosing canine visceral leishmaniasis (CVL). Ninety-two dogs exhibiting leishmaniasis seroreactivity were evaluated. The animals were euthanized; and healthy skin, spleen, popliteal lymph node, and BM puncture samples were cultured. BM cultures were used as the reference standard. Of the 92 dogs studied, 85.9% exhibited positive cultures, and Leishmania infantum (synonym Leishmania chagasi) was confirmed in all positive culture cases. The sensitivity rates for cytocentrifugation as well as thin and thick smears were 47.1%, 52.8%, and 77%, respectively. However, no association between the dogs' clinical status and culture or direct examination results was found. To our knowledge, this was the first study to use thick smears and cytocentrifugation for diagnosing CVL. Our results indicate that BM thick smears have a good sensitivity and their use reduces the time required to read slides. Therefore, thick smears can provide a rapid and safe alternative to parasitological confirmation of seroreactive dogs

Sporothrix schenckii sensu lato identification in fragments of skin lesion cultured in NNN medium for differential diagnosis of cutaneous leishmaniasis

Submitted by Janaína Nascimento ([email protected]) on 2019-02-21T12:29:32Z No. of bitstreams: 1 ve_Antonio_Liliane_etal_INI_2017.pdf: 296871 bytes, checksum: 837e86c8b528bc274edcd2a9355f02ee (MD5)Approved for entry into archive by Janaína Nascimento ([email protected]) on 2019-02-21T13:20:28Z (GMT) No. of bitstreams: 1 ve_Antonio_Liliane_etal_INI_2017.pdf: 296871 bytes, checksum: 837e86c8b528bc274edcd2a9355f02ee (MD5)Made available in DSpace on 2019-02-21T13:20:28Z (GMT). No. of bitstreams: 1 ve_Antonio_Liliane_etal_INI_2017.pdf: 296871 bytes, checksum: 837e86c8b528bc274edcd2a9355f02ee (MD5) Previous issue date: 2017Fundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica e Vigilância em Leishmanioses. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica e Vigilância em Leishmanioses. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica e Vigilância em Leishmanioses. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica e Vigilância em Leishmanioses. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Micologia. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Micologia. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Micologia. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica e Vigilância em Leishmanioses. Rio de Janeiro, RJ, Brasil / Fellow researcher of Conselho Nacional de Desenvolvimento Científico e Tecnológico. Brasília, DF, Brasil / Fellow researcher “Cientista do Nosso Estado” of Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro. Rio de Janeiro, RJ, Brazil.Eighty-nine patients with clinical suspicion of leishmaniasis were referred for differential diagnosis. Sporothrix schenckii sensu lato was isolated in Novy-MacNeal-Nicolle + Schneider media in 98% of 64 patients with final diagnosis of sporotrichosis. This medium may be suitable for diagnosis of sporotrichosis in areas where cutaneous leishmaniasis is also endemic