RealROC: a shiny based application for ROC curve study with covariate adjustment

Dissertação de mestrado em BioinformaticsA curva ROC (Receiver operating characteristic) é uma ferramenta analítica eficaz para testes clínicos. A análise permite visualizar a variação de sensibilidade e especificidade para uma dada região de corte através de um simples, mas robusto gráfico bidimensional. Num contexto biológico, testes podem ser influenciados por múltiplas variáveis externas e como tal a análise ROC pode não ser a ideal ou gerar resultados incompletos. É então necessário saber que variáveis afetam determinado teste clínico de forma a determinar os melhores parâmetros para determinado teste ou até descartar determinada metodologia mediante a situação. O ajuste da curva ROC a covariáveis permite a normalização do efeito das mesmas ou diretamente ajustar a curva para os seus efeitos. Software direcionado ao ajuste da curva ROC é, infelizmente, escasso e muitas vezes difícil de manusear por utilizadores não especializados. Recentemente o pacote AROC foi lançando para R que disponibiliza vários recursos para estes ajustamentos, no entanto a dificuldade de utilização mantém-se. A combinação deste pacote com a estrutura Shiny, um pacote que permite o desenvolvimento de aplicações interativas, tem por objetivo a criação de um programa grátis e acessível que permita uma análise mais aprofundada disponível para todos os investigadores. RealROC foi capaz de replicar resultados de um caso de estudo que analisou a influência do sexo no sistema de pontuação CRIB e respetiva previsão de mortalidade, demonstrando a usabilidade e acessibilidade do programa que será disponibilizado online e potencialmente contribuir para novos desenvolvimentos na área.Receiver operating characteristic (ROC) curves are a powerful analytical tool for clinical tests. The analysis allows the visualization of varying sensitivity and specificity for a given threshold through a simple, yet robust, two-dimensional plot. In a biological framework, tests can be influenced by multiple external variables, as such, standard ROC analysis may not be suitable or may provide incomplete data. It is then necessary to know which variables influence clinical test results to determine optimal conditions for trials or even to disregard a given method of evaluation in certain contexts. Adjusting for covariates allows ROC analysis to normalize the effects of the variable in question or to directly adjust the curve for its effects. Unfortunately ROC software that is able to conduct such an adjustment is sparse and proven difficult to use for non technical users. Recently, the AROC package for R was released and provides a robust resource for such adjustments however with he same usability problems previously stated. By combining this package with the Shiny framework, an R package that allows the creation of interactive applications, we hope to provide an accessible and free software that allows this extra depth of analysis to be available for all researchers. RealROC was able to mimic the results of a case study analysing the affects of sex to the CRIB score and resulting mortality rates that proving its practicality and will be made available online and hopefully contribute to the advancement of software in this field

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

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

Exílio escravista: Hercule Florence e as fronteiras do açúcar e do café no Oeste paulista (1830-1879)

RESUMO O artigo investiga a trajetória do artista e inventor Antonie Hercule Romuald Florence (1804-1879) na sociedade escravista brasileira do século XIX, procurando examinar os fundamentos do "sentimento de exílio" que marcou sua longa vivência no Oeste de São Paulo. Na primeira parte, trato Florence como um observador das paisagens escravistas do açúcar e do café. A série de desenhos e aquarelas que compôs sobre a fazenda Ibicaba e o engenho da Cachoeira nos permite observar como ele apreendeu os processos concretos de transformação agrária e ambiental da fronteira escravista de São Paulo. Na segunda parte, analiso a conversão de Florence em cafeicultor escravista, momento em ele assumiu por razões familiares a gestão de uma propriedade cafeeira com trinta escravos no município de Campinas

Comentarios a una sentencia anunciada : el proceso Lula

El centenar de textos que conforman este libro -escritos por un movimiento de prestigiosos/as juristas y abogados- desgranan el procedimiento al que fue sometido Lula. En la opinión de las y los autores de los artículos las normas no fueron observadas, y su inobservancia llevó a que se dictaminase una decisión injusta. Frases del estilo "Voy a tomar una decisión revolucionaria, dejando de lado la ley, porque por la ley no se puede condenarlo de ninguna manera”, dichas en los juicios por las más altas autoridades judiciales militares y civiles, hoy son conocidas gracias a quienes se abocaron al trabajo de escuchar los audios de aquellas sesiones, nutriendo las reflexiones que argumentan sobre el imperativo de la hora: restablecer el estado de derecho y absolver al presidente Lula Da Silva

Comentários a uma sentença anunciada : o processo Lula

“Comentários a uma sentença: o Caso Lula” é talvez o mais importante documento jurídico publicado no Brasil em décadas. A presente coletânea de artigos nasceu de um movimento espontâneo e bastante significativo de juristas brasileiros e estrangeiros que examinaram cuidadosamente a sentença proferida no âmbito do processo que tramitou na 13ª Vara Federal de Curitiba, no caso que ficou conhecido na mídia como o do “tríplex do Guarujá”. <br>De la presentación de Geraldo Prad

NEOTROPICAL ALIEN MAMMALS: a data set of occurrence and abundance of alien mammals in the Neotropics

Biological invasion is one of the main threats to native biodiversity. For a species to become invasive, it must be voluntarily or involuntarily introduced by humans into a nonnative habitat. Mammals were among first taxa to be introduced worldwide for game, meat, and labor, yet the number of species introduced in the Neotropics remains unknown. In this data set, we make available occurrence and abundance data on mammal species that (1) transposed a geographical barrier and (2) were voluntarily or involuntarily introduced by humans into the Neotropics. Our data set is composed of 73,738 historical and current georeferenced records on alien mammal species of which around 96% correspond to occurrence data on 77 species belonging to eight orders and 26 families. Data cover 26 continental countries in the Neotropics, ranging from Mexico and its frontier regions (southern Florida and coastal-central Florida in the southeast United States) to Argentina, Paraguay, Chile, and Uruguay, and the 13 countries of Caribbean islands. Our data set also includes neotropical species (e.g., Callithrix sp., Myocastor coypus, Nasua nasua) considered alien in particular areas of Neotropics. The most numerous species in terms of records are from Bos sp. (n = 37,782), Sus scrofa (n = 6,730), and Canis familiaris (n = 10,084); 17 species were represented by only one record (e.g., Syncerus caffer, Cervus timorensis, Cervus unicolor, Canis latrans). Primates have the highest number of species in the data set (n = 20 species), partly because of uncertainties regarding taxonomic identification of the genera Callithrix, which includes the species Callithrix aurita, Callithrix flaviceps, Callithrix geoffroyi, Callithrix jacchus, Callithrix kuhlii, Callithrix penicillata, and their hybrids. This unique data set will be a valuable source of information on invasion risk assessments, biodiversity redistribution and conservation-related research. There are no copyright restrictions. Please cite this data paper when using the data in publications. We also request that researchers and teachers inform us on how they are using the data

Brazilian Flora 2020: Leveraging the power of a collaborative scientific network

International audienceThe shortage of reliable primary taxonomic data limits the description of biological taxa and the understanding of biodiversity patterns and processes, complicating biogeographical, ecological, and evolutionary studies. This deficit creates a significant taxonomic impediment to biodiversity research and conservation planning. The taxonomic impediment and the biodiversity crisis are widely recognized, highlighting the urgent need for reliable taxonomic data. Over the past decade, numerous countries worldwide have devoted considerable effort to Target 1 of the Global Strategy for Plant Conservation (GSPC), which called for the preparation of a working list of all known plant species by 2010 and an online world Flora by 2020. Brazil is a megadiverse country, home to more of the world's known plant species than any other country. Despite that, Flora Brasiliensis, concluded in 1906, was the last comprehensive treatment of the Brazilian flora. The lack of accurate estimates of the number of species of algae, fungi, and plants occurring in Brazil contributes to the prevailing taxonomic impediment and delays progress towards the GSPC targets. Over the past 12 years, a legion of taxonomists motivated to meet Target 1 of the GSPC, worked together to gather and integrate knowledge on the algal, plant, and fungal diversity of Brazil. Overall, a team of about 980 taxonomists joined efforts in a highly collaborative project that used cybertaxonomy to prepare an updated Flora of Brazil, showing the power of scientific collaboration to reach ambitious goals. This paper presents an overview of the Brazilian Flora 2020 and provides taxonomic and spatial updates on the algae, fungi, and plants found in one of the world's most biodiverse countries. We further identify collection gaps and summarize future goals that extend beyond 2020. Our results show that Brazil is home to 46,975 native species of algae, fungi, and plants, of which 19,669 are endemic to the country. The data compiled to date suggests that the Atlantic Rainforest might be the most diverse Brazilian domain for all plant groups except gymnosperms, which are most diverse in the Amazon. However, scientific knowledge of Brazilian diversity is still unequally distributed, with the Atlantic Rainforest and the Cerrado being the most intensively sampled and studied biomes in the country. In times of “scientific reductionism”, with botanical and mycological sciences suffering pervasive depreciation in recent decades, the first online Flora of Brazil 2020 significantly enhanced the quality and quantity of taxonomic data available for algae, fungi, and plants from Brazil. This project also made all the information freely available online, providing a firm foundation for future research and for the management, conservation, and sustainable use of the Brazilian funga and flora