Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Biochronostratigraphy and paleoenvironment analysis of Neogene deposits from the Pelotas Basin (well 2-TG-96-RS), Southernmost Brazil

This paper presents the integration of micropaleontological (palynology and foraminifera) and isotopic (87Sr/86Sr) analysis of a selected interval from the well 2-TG-96-RS, drilled on the onshore portion of the Pelotas Basin, Rio Grande do Sul, Brazil. A total of eight samples of the section between 140.20 and 73.50 m in depth was selected for palynological analysis, revealing diversified and abundant palynomorph associations. Species of spores, pollen grains and dinoflagellate cysts are the most common palynomorphs found. Planktic and benthic calcareous foraminifera were recovered from the lowest two levels of the section (140.20 and 134.30 m). Based on the stratigraphic range of the species of dinoflagellate cysts and sporomorphs, a span age from Late Miocene to Early Pliocene is assigned. The relative age obtained from the 87Sr/86Sr ratio in shells of calcareous foraminifers indicates a Late Miocene (Messinian) correspondence, corroborating the biostratigraphic positioning performed with palynomorphs. Paleoenvironmental interpretations based on the quantitative distribution of organic components (palynomorphs, phytoclasts and amorphous organic matter) throughout the section and on foraminiferal associations indicate a shallow marine depositional environment for the section. Two palynologicals intervals were recognized based on palynofacies analysis, related to middle to outer shelf (140.20 to 128.90 m) and inner shelf (115.75 to 73.50 m) conditions

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Distribuição e identificação das regiões de risco para a cisticercose bovina no estado do Paraná

A cisticercose bovina é um problema de saúde pública e animal amplamente difundido no Brasil, que repercute negativamente na produção de carne em diversos estados do país. Trata-se de uma das afecções mais ocorrentes nos abates sob inspeção sanitária tornando-se motivo de preocupação para frigoríficos e produtores, devido os prejuízos que acarreta. Pouco se conhece sobre a distribuição e a evolução do número de casos de cisticercose bovina no estado do Paraná. Diante do exposto este trabalho teve o objetivo realizar um levantamento retrospectivo sobre a ocorrência da cisticercose bovina, diagnosticada através do exame post-mortem pelo Serviço de Inspeção Federal do Estado do Paraná entre os anos de 2004 a 2008, além de determinar a distribuição dos casos no Estado, identificar as regiões com maiores chances de apresentarem casos da doença e analisar a perda econômica do Estado por conta das condenações por esta parasitose. Foi constatada prevalência de 2,23% cisticercose bovina no estado do Paraná. Durante o período analisado ocorreu uma redução estatisticamente significante (p<0,05) da prevalência de cisticercose bovina no estado. Nos anos de 2004-2008 foram condenadas 29.708.550 kg de carne bovina por cisticercose, acarretando prejuízos de ordem econômica. O estado do Paraná está conseguindo através da implantação do programa de controle do complexo teníase-cisticercose, uma evolução positiva já que conseguiu durante o período analisado diminuir a prevalência desta parasitose nos bovinos e consequentemente diminuir as perdas econômicas

Epidemiological survey of the taeniasis/cysticercosis complex in cattle farms in Viçosa County, Minas Gerais, Brazil Inquérito epidemiológico sobre o complexo teníase-cisticercose bovina no município de Viçosa, Minas Gerais

Despite the importance of human taeniasis/bovine cysticercosis for public and animal health and the economy, its actual epidemiological status in Brazil is not well-studied. We sought to assess the epidemiological profile of this zoonosis in the rural area of Viçosa County, Minas Gerais, Brazil. The prevalence of bovine cysticercosis was 0.42%, whereas no case of human taeniasis was diagnosed. Factors favoring the persistence of zoonosis were identified. These included the supply of untreated water to animals, animals raised for slaughter without sanitary supervision, poor mechanization of raising techniques, and the use of untreated water for human consumption. Bovine meat for human consumption acquired in the city or from the farm itself was characterized as a risk factor for bovine cysticercosis (Odds Ratio (OR) =16.77; p<0.05). Nevertheless, the families on the investigated farms did apply several appropriate measures to control this disease, such as the virtual lack of open sewers and the consumption of well-cooked meat. The presence of bovine cysticercosis cases, and the factors favoring its persistence, point to the need for constant epidemiological and sanitary surveillance in this county.<br>Apesar da importância do complexo teníase-cisticercose bovina para a saúde pública, animal e para a economia, a realidade epidemiológica da ocorrência dessas zoonoses no Brasil é pouco conhecida. Este estudo foi realizado com o objetivo de avaliar o perfil epidemiológico desta zoonose na zona rural do município de Viçosa, MG. A prevalência encontrada de cisticercose bovina foi de 0,42%, e nenhum caso de teníase humana foi diagnosticado. Foi verificada presença de fatores favoráveis a manutenção dessa zoonose, como fornecimento de água sem tratar aos animais, criação de animais destinados ao abate sem inspeção sanitária, criação de bovinos com baixa adoção de tecnologia, e utilização de água sem tratamento. O consumo de carne bovina oriunda da propriedade e da cidade foi caracterizado como variável de risco (OR=16,77; p<0,05) para a cisticercose bovina. Apesar disso, as famílias das propriedades pesquisadas possuíam hábitos favoráveis como medida de controle para o desenvolvimento desta parasitose, como a quase ausência de esgoto a céu aberto e a ingestão de carne bovina bem passada. A presença de caso de cisticercose bovina e de fatores considerados favoráveis a manutenção dessa parasitose, mostra a necessidade da contínua vigilância epidemiológica e sanitária neste município

Epidemiological survey of the taeniasis/cysticercosis complex in cattle farms in Viçosa County, Minas Gerais, Brazil

Despite the importance of human taeniasis/bovine cysticercosis for public and animal health and the economy, its actual epidemiological status in Brazil is not well-studied. We sought to assess the epidemiological profile of this zoonosis in the rural area of Viçosa County, Minas Gerais, Brazil. The prevalence of bovine cysticercosis was 0.42%, whereas no case of human taeniasis was diagnosed. Factors favoring the persistence of zoonosis were identified. These included the supply of untreated water to animals, animals raised for slaughter without sanitary supervision, poor mechanization of raising techniques, and the use of untreated water for human consumption. Bovine meat for human consumption acquired in the city or from the farm itself was characterized as a risk factor for bovine cysticercosis (Odds Ratio (OR) =16.77; p<0.05). Nevertheless, the families on the investigated farms did apply several appropriate measures to control this disease, such as the virtual lack of open sewers and the consumption of well-cooked meat. The presence of bovine cysticercosis cases, and the factors favoring its persistence, point to the need for constant epidemiological and sanitary surveillance in this county

Prevalence and risk factors for porcine cysticercosis in rural communities of eastern Minas Gerais, Brazil

ABSTRACT: Cysticercosis is caused by Taenia solium, a parasitic zoonosis that affects human and pigs raised free-range in developing countries. The epidemiology of the taeniosis cysticercosis complex in Brazil is poorly understood especially when it comes to field research. The aim of this study was to estimate the prevalence and identify the risk factors associated with porcine cysticercosis in rural communities located in the east of Minas Gerais (MG), Brazil. From 371 farms in the county of Tumiritinga/MG, 101 farms from 14 communities were randomly sampled. Blood samples from pigs were collected, and epidemiological questionnaires were carried out. The serum samples obtained were analyzed through immunodiagnosis techniques, including ELISA and Western Blot, both for the detection of antibodies. The data obtained by different surveys were analyzed using EpiInfo 3.5.1 software to determine seroprevalence and risk factors associated with cysticercosis. The prevalence of farms with porcine cysticercosis was 9.9% (10/101) and antibody-based seropositive was 5.3% (13/247). The results indicate that cysticercosis occurs in high level in the rural area never studied before. These results suggest the presence of tapeworm carriers contributing to the occurrence and maintenance of this zoonotic life cycle in the county. Regarding risk factors, the most significant determinants for porcine cysticercosis in the field were free-range pig management (OR: 17.4, p: 0.0001), the method of disposal of human faeces in the environmental (OR: 7.6; p 0.012), and the size of the farm. Porcine cysticercosis was diagnosed only in areas represented by Agrarian Reform Settlements. From the results, it is possible to recommend as a means of control and prevention the destination of human faeces in appropriate sanitary landfills and the production of pigs in an enclosed area. Additionally, improving education in the communities sampled will indirectly affect the spreading of this disease. The results draw attention to the largest studies of this zoonotic disease in human settlements from rural areas due to the lack of knowledge about the epidemiology of the taeniosis-cysticercosis complex. The results could serve as the basis to support public policies aimed at creating an effective program to control the taeniosis-cysticercosis complex in the studied area. Awareness of TC among medical doctors, veterinarians, meat animal family producers and the public should be developed through appropriate information and education