Every fifth published metagenome is not available to science

Have you ever sought to use metagenomic DNA sequences reported in scientific publications? Were you successful? Here, we reveal that metagenomes from no fewer than 20% of the papers found in our literature search, published between 2016 and 2019, were not deposited in a repository or were simply inaccessible. The proportion of inaccessible data within the literature has been increasing year-on-year. Noncompliance with Open Data is best predicted by the scientific discipline of the journal. The number of citations, journal type (e.g., Open Access or subscription journals), and publisher are not good predictors of data accessibility. However, many publications in high–impact factor journals do display a higher likelihood of accessible metagenomic data sets. Twenty-first century science demands compliance with the ethical standard of data sharing of metagenomes and DNA sequence data more broadly. Data accessibility must become one of the routine and mandatory components of manuscript submissions—a requirement that should be applicable across the increasing number of disciplines using metagenomics. Compliance must be ensured and reinforced by funders, publishers, editors, reviewers, and, ultimately, the authors.info:eu-repo/semantics/publishedVersio

[Performance by cytology and hybrid capture II in screening for high-grade squamous intraepithelial lesions in women with HIV].

HIV-infected women are at increased risk of developing high-grade squamous intraepithelial lesions (HSIL), the precursor lesions for cervical cancer. This study estimated and compared the performance of cytology and hybrid capture II in screening for precursor lesions of cervical cancer among HIV-infected women. The study population consisted of women from the open prospective cohort at the Evandro Chagas Clinical Research Institute, Oswaldo Cruz Foundation (IPEC/Fiocruz). Colposcopy and histology were considered jointly in defining the gold standard. Cytology showed 31.8% sensitivity and 95.5% specificity, while hybrid capture II showed higher sensitivity (100%) and lower specificity (52%). The positive likelihood ratio was 7.1 for cytology and 2.1 for hybrid capture II, while the negative likelihood ratio was 0.7 for cytology and 0.0 for hybrid capture II

Prevalência de neoplasia intra-epitelial cervical graus II/III e câncer cervical nas pacientes com diagnóstico citológico de células escamosas atípicas, quando não se pode excluir lesão intra-epitelial de alto grau (ASC-H)

CONTEXTO E OBJETIVO:A última atualização do Sistema Bethesda dividiu a categoria de células escamosas atípicas de significado indeterminado (ASCUS) em ASC-US (de significado indeterminado) e ASC-H (quando não se pode excluir lesão intra-epitelial de alto grau). Os objetivos deste estudo foram medir a prevalência da lesão pré-invasiva (Neoplasia Intra-epitelial Cervical, NIC II/III) e câncer cervical, de pacientes que foram encaminhadas ao Instituto Fernandes Figueira (IFF), com citologia ASC-H e compará-la com os casos ASC-US. TIPO DE ESTUDO E LOCAL:Estudo transversal com coleta de dados retrospectiva, que ocorreu no ambulatório de Patologia Cervical do IFF. MÉTODOS:Casos com diagnóstico de ASCUS recebidos no IFF entre novembro de 1997 a setembro de 2007, foram revisados de acordo com o Sistema Bethesda 2001 até um diagnóstico de consenso. Os casos ASC-H e ASC-US resultantes desta revisão, e os casos novos, foram analisados em relação ao desfecho de interesse. Consideramos padrão-ouro tanto a histologia como, nos casos sem diagnóstico histológico, o acompanhamento cito-colposcópico. RESULTADOS:A prevalência de NIC II/III na citologia ASC-H foi de 19,29% (intervalo de confiança, IC 95% 9,05-29,55%) e o risco destas lesões foi maior entre as pacientes com citologia ASC-H comparado às pacientes com citologia ASC-US (razão de prevalência, RP = 10,42; IC 95% 2,39-45,47; P = 0,0000764). A lesão pré-invasiva na citologia ASC-H foi mais frequente abaixo dos 50 anos (RP = 2,67; IC 95% 0,38-18,83), P = 0,2786998. Não houve casos de câncer do colo do útero. CONCLUSÕES:A prevalência de NIC II/III em pacientes com citologia ASC-H foi significativamente mais alta que a de ASC-US, e a divisão em subcategorias do diagnóstico ASC se mostrou com boa capacidade para discriminar a presença de lesões pré invasivas.CONTEXT AND OBJECTIVE:The latest update of the Bethesda System divided the category of atypical squamous cells of undetermined significance (ASCUS) into ASC-US (undetermined significance) and ASC-H (high-grade intraepithelial lesion cannot be ruled out). The aims here were to measure the prevalence of pre-invasive lesions (cervical intraepithelial neoplasia, CIN II/III) and cervical cancer among patients referred to Instituto Fernandes Figueira (IFF) with ASC-H cytology, and compare them with ASC-US cases. DESIGN AND SETTING:Cross-sectional study with retrospective data collection, at the IFF Cervical Pathology outpatient clinic. METHODS:ASCUS cases referred to IFF from November 1997 to September 2007 were reviewed according to the 2001 Bethesda System to reach cytological consensus. The resulting ASC-H and ASC-US cases, along with new cases, were analyzed relative to the outcome of interest. The histological diagnosis (or cytocolposcopic follow-up in cases without such diagnosis) was taken as the gold standard. RESULTS:The prevalence of CIN II/III in cases with ASC-H cytology was 19.29% (95% confidence interval, CI, 9.05-29.55%) and the risk of these lesions was greater among patients with ASC-H than with ASC-US cytology (prevalence ratio, PR, 10.42; 95% CI, 2.39-45.47; P = 0.0000764). Pre-invasive lesions were more frequently found in patients under 50 years of age with ASC-H cytology (PR, 2.67; 95% CI, 0.38-18.83); P = 0.2786998). There were no uterine cervical cancer cases. CONCLUSION:The prevalence of CIN II/III in patients with ASC-H cytology was significantly higher than with ASC-US, and division into ASC diagnostic subcategories had good capacity for discriminating the presence of pre-invasive lesions

Predictors of early menopause in HIV-infected women: a prospective cohort study

This study sought to investigate the age at natural menopause and its predictors in a cohort of human immunodeficiency virus (HIV)-infected women in Rio de Janeiro, Brazil.2028-08-3

Potential drivers of the proportion of papers with accessible data for each journal.

Potential drivers of the proportion of papers with accessible data for each journal.</p

Main trends in accessibility of metagenomic data.

(A) Proportion of papers with accessible metagenomic data and type of inaccessible data (grey) (B) in B, M, or T journals. (C) Temporal trends divided by B, M, and T journals. B, biological; M, multidisciplinary; T, technological.</p

Absence of effect of menopause status at initiation of first-line antiretroviral therapy on immunologic or virologic responses: a cohort study from Rio de Janeiro, Brazil

Submitted by Rodrigo Senorans ([email protected]) on 2015-06-26T15:31:26Z No. of bitstreams: 1 Absence of effect of menopause status at initiation of first-line antiretroviral therapy on immunologic or virologic responses A cohort study from Rio de Janeiro, Brazil.pdf: 104692 bytes, checksum: 5af38dd1e354452d045751ee4890aa9e (MD5)Approved for entry into archive by Anderson Silva ([email protected]) on 2015-07-03T12:57:17Z (GMT) No. of bitstreams: 1 Absence of effect of menopause status at initiation of first-line antiretroviral therapy on immunologic or virologic responses A cohort study from Rio de Janeiro, Brazil.pdf: 104692 bytes, checksum: 5af38dd1e354452d045751ee4890aa9e (MD5)Approved for entry into archive by Anderson Silva ([email protected]) on 2015-07-03T12:57:26Z (GMT) No. of bitstreams: 1 Absence of effect of menopause status at initiation of first-line antiretroviral therapy on immunologic or virologic responses A cohort study from Rio de Janeiro, Brazil.pdf: 104692 bytes, checksum: 5af38dd1e354452d045751ee4890aa9e (MD5)Made available in DSpace on 2015-07-06T13:06:45Z (GMT). No. of bitstreams: 1 Absence of effect of menopause status at initiation of first-line antiretroviral therapy on immunologic or virologic responses A cohort study from Rio de Janeiro, Brazil.pdf: 104692 bytes, checksum: 5af38dd1e354452d045751ee4890aa9e (MD5) Previous issue date: 2014Fundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica em DST e AIDS. Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica em DST e AIDS. Rio de Janeiro, RJ, Brasil / Universidade Federal do Estado do Rio de Janeiro. Departamento de Matemática e Estatística. Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica em DST e AIDS. Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica em DST e AIDS. Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica em DST e AIDS. Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica em DST e AIDS. Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica em DST e AIDS. Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica em DST e AIDS. Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica em DST e AIDS. Rio de Janeiro, RJ, BrasilObjective: To compare the effectiveness of first-line combination antiretroviral therapy (cART) between premenopausal and postmenopausal women. Methods: ART-naı¨ve women initiating cART between January 2000/June 2010 at the Instituto de Pesquisa Clı´nica Evandro Chagas Cohort were studied. Women were defined as postmenopausal after 12 consecutive months of amenorrhea. CD4 cell counts and HIV-1 RNA viral load (VL) measurements were compared between pre- and postmenopausal at 6, 12 and 24 months after cART initiation. Women who modified/discontinued a drug class or died due to an AIDS defining illness were classified as ART-failures. Variables were compared using Wilcoxon test, x2 or Fisher’s exact test. The odds of cART effectiveness (VL,400 copies/mL and/or no need to change cART) were compared using logistic regression. Linear model was used to access relationship between CD4 change and menopause. Results: Among 383 women, 328 (85%) were premenopausal and 55 (15%) postmenopausal. Median pre cART CD4 counts were 231 and 208 cells/mm3 (p=0.14) in pre- and postmenopausal women, respectively. No difference in the median pre cART VL was found (both 4.8 copies/mL). Median CD4 changes were similar at 6 and 12 months. At 24 months after cART initiation, CD4 changes among postmenopausal women were significantly lower among premenopausal women (p=0.01). When the analysis was restricted to women with VL,400 copies/mL, no statistical difference was observed. Overall, 63.7% achieved cART effectiveness at 24 months without differences between groups at 6, 12 and 24 months. Conclusion: Menopause status at the time of first-line cART initiation does not impact CD4 cell changes at 24 months among women with a virologic response. No relationship between menopause status and virologic response was observed

cART effectiveness and CD4 change models at 6, 12, and 24 months for premenopausal and postmenopausal antiretroviral-naïve women.

<p>cART: Combination Antiretroviral Therapy; OR: Odds Ratio.</p><p>Models adjusted for baseline log 10 HIV-1 RNA levels, baseline CD4, HAART regimen and AIDS defining illness.</p><p>p<0.05 in bold.</p