cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7075472.v1
title: De novo transcriptome assembly of the lobster cockroach Nauphoeta cinerea (Blaberidae)

description: Abstract The use of Drosophila as a scientific model is well established, but the use of cockroaches as experimental organisms has been increasing, mainly in toxicology research. Nauphoeta cinerea is one of the species that has been studied, and among its advantages is its easy laboratory maintenance. However, a limited amount of genetic data about N. cinerea is available, impeding gene identification and expression analyses, genetic manipulation, and a deeper understanding of its functional biology. Here we describe the N. cinerea fat body and head transcriptome, in order to provide a database of genetic sequences to better understand the metabolic role of these tissues, and describe detoxification and stress response genes. After removing low-quality sequences, we obtained 62,121 transcripts, of which more than 50% had a length of 604 pb. The assembled sequences were annotated according to their genes ontology (GO). We identified 367 genes related to stress and detoxification; among these, the more frequent were p450 genes. The results presented here are the first large-scale sequencing of N. cinerea and will facilitate the genetic understanding of the species' biochemistry processes in future works.
DOI: 10.6084/m9.figshare.7075469.v1
title: Development of a comprehensive noninvasive prenatal test

description: Abstract Our aim was to develop and apply a comprehensive noninvasive prenatal test (NIPT) by using high-coverage targeted next-generation sequencing to estimate fetal fraction, determine fetal sex, and detect trisomy and monogenic disease without parental genotype information. We analyzed 45 pregnancies, 40 mock samples, and eight mother-child pairs to generate 35 simulated datasets. Fetal fraction (FF) was estimated based on analysis of the single nucleotide polymorphism (SNP) allele fraction distribution. A Z-score was calculated for trisomy of chromosome 21 (T21), and fetal sex detection. Monogenic disease detection was performed through variant analysis. Model validation was performed using the simulated datasets. The novel model to estimate FF was robust and accurate (r2= 0.994, p-value &lt; 2.2e-16). For samples with FF &gt; 0.04, T21 detection had 100% sensitivity (95% CI: 63.06 to 100%) and 98.53% specificity (95% CI: 92.08 to 99.96%). Fetal sex was determined with 100% accuracy. We later performed a proof of concept for monogenic disease diagnosis of 5/7 skeletal dysplasia cases. In conclusion, it is feasible to perform a comprehensive NIPT by using only data from high coverage targeted sequencing, which, in addition to detecting trisomies, also make it possible to identify pathogenic variants of the candidate genes for monogenic diseases.
DOI: 10.6084/m9.figshare.7075463
title: Can plant DNA barcoding be implemented in species-rich tropical regions? A perspective from São Paulo State, Brazil

description: Abstract DNA barcoding helps to identify species, especially when identification is based on parts of organisms or life stages such as seeds, pollen, wood, roots or juveniles. However, the implementation of this approach strongly depends on the existence of complete reference libraries of DNA sequences. If such a library is incomplete, DNA-based identification will be inefficient. Here, we assess if DNA barcoding can already be implemented in species-rich tropical regions. We focus on the tree flora of São Paulo state, Brazil, which contains more than 2000 tree species. Using new DNA sequence data and carefully assembled GenBank accessions, we assembled 12,113 sequences from ten different regions. The ITS, rbcL, psbA-trnH, matK and trnL regions were better represented within the available sequences for São Paulo tree flora. Currently, only 58% of the São Paulo tree flora currently have at least one barcoding sequence available. However, these species represent on average 89% of the trees in São Paulo state forests. Therefore, conservation-oriented and ecological studies can already benefit from DNA barcoding to obtain more accurate species identifications. We present which taxa remain underrepresented for the São Paulo tree flora and discuss the implications of this result for other species-rich tropical regions.
DOI: 10.6084/m9.figshare.7075466
title: Spatial self-phase modulation: a second instructive and low-cost demonstration of a nonlinear optical effect

description: Abstract The traditional teaching of general physics at undergraduate level usually restricts to linear optics, neglecting the nonlinear optics which plays an increasingly important role in several areas of technological development. This paper discusses the proposal of a simple and low cost experiment for the demonstration of the nonlinear optical effect called spatial self-phase modulation. This experiment completes the proposal of low cost experiments in the demonstration of nonlinear optical effects that began with the demonstration of the so-called thermal lens in a previous paper. Spatial self-phase modulation is based on the introduction of an additional term in the phase of a Gaussian wave incident on a medium as a consequence of its heating by the beam. As a nonlinear medium it is proposed to use a simple and low cost fluid such as soy sauce (shoyu sauce), whole grape juice or cola soft drink.
DOI: 10.26165/juelich-data/tvwuup/t2ew7f
title: 141.png

description: :unav
DOI: 10.6084/m9.figshare.7075466.v1
title: Spatial self-phase modulation: a second instructive and low-cost demonstration of a nonlinear optical effect

description: Abstract The traditional teaching of general physics at undergraduate level usually restricts to linear optics, neglecting the nonlinear optics which plays an increasingly important role in several areas of technological development. This paper discusses the proposal of a simple and low cost experiment for the demonstration of the nonlinear optical effect called spatial self-phase modulation. This experiment completes the proposal of low cost experiments in the demonstration of nonlinear optical effects that began with the demonstration of the so-called thermal lens in a previous paper. Spatial self-phase modulation is based on the introduction of an additional term in the phase of a Gaussian wave incident on a medium as a consequence of its heating by the beam. As a nonlinear medium it is proposed to use a simple and low cost fluid such as soy sauce (shoyu sauce), whole grape juice or cola soft drink.
DOI: 10.26165/juelich-data/tvwuup/ymzkna
title: 317.png

description: :unav
DOI: 10.6084/m9.figshare.7075463.v1
title: Can plant DNA barcoding be implemented in species-rich tropical regions? A perspective from São Paulo State, Brazil

description: Abstract DNA barcoding helps to identify species, especially when identification is based on parts of organisms or life stages such as seeds, pollen, wood, roots or juveniles. However, the implementation of this approach strongly depends on the existence of complete reference libraries of DNA sequences. If such a library is incomplete, DNA-based identification will be inefficient. Here, we assess if DNA barcoding can already be implemented in species-rich tropical regions. We focus on the tree flora of São Paulo state, Brazil, which contains more than 2000 tree species. Using new DNA sequence data and carefully assembled GenBank accessions, we assembled 12,113 sequences from ten different regions. The ITS, rbcL, psbA-trnH, matK and trnL regions were better represented within the available sequences for São Paulo tree flora. Currently, only 58% of the São Paulo tree flora currently have at least one barcoding sequence available. However, these species represent on average 89% of the trees in São Paulo state forests. Therefore, conservation-oriented and ecological studies can already benefit from DNA barcoding to obtain more accurate species identifications. We present which taxa remain underrepresented for the São Paulo tree flora and discuss the implications of this result for other species-rich tropical regions.
DOI: 10.26165/juelich-data/tvwuup/5iyxm4
title: 609.png

description: :unav
DOI: 10.26165/juelich-data/tvwuup/anmknx
title: 718.png

description: :unav
DOI: 10.26165/juelich-data/tvwuup/l6fcea
title: 373.png

description: :unav
DOI: 10.26165/juelich-data/tvwuup/4hubua
title: 387.png

description: :unav
DOI: 10.6084/m9.figshare.7075442
title: Misadventures of media influence in post-1988 Brazil: a theory of political information demand

description: Abstract The article presents a theory of political information demand, and its model is applied to the analysis of the seven Brazilian presidential elections following the transition to democracy. The initial goal of the theory is to posit the potential of the political and electoral influence of the mass media on the choices not only of so-called ordinary citizens, but also of militants, depending on the political and institutional context. In other words, why does intervention on the part of the mass media in certain circumstances seem to have a decisive influence on the choices of some individuals but not in others? How does one discern such variations without the known limits of political information supply analyses, which either do not account for the reception’s polysemy, or, which cannot be generalized when they do, on a smaller scale and with more depth. According to this theory, media influence is a function of the utility attributed to political information, which depends on the stability and intensity of voter preferences and the risk margins with which they make their decisions, which in turn depend on the overall stability and degree of political polarization of the political system. Some of the other potentials of the theory are also briefly indicated.
DOI: 10.6084/m9.figshare.7075442.v1
title: Misadventures of media influence in post-1988 Brazil: a theory of political information demand

description: Abstract The article presents a theory of political information demand, and its model is applied to the analysis of the seven Brazilian presidential elections following the transition to democracy. The initial goal of the theory is to posit the potential of the political and electoral influence of the mass media on the choices not only of so-called ordinary citizens, but also of militants, depending on the political and institutional context. In other words, why does intervention on the part of the mass media in certain circumstances seem to have a decisive influence on the choices of some individuals but not in others? How does one discern such variations without the known limits of political information supply analyses, which either do not account for the reception’s polysemy, or, which cannot be generalized when they do, on a smaller scale and with more depth. According to this theory, media influence is a function of the utility attributed to political information, which depends on the stability and intensity of voter preferences and the risk margins with which they make their decisions, which in turn depend on the overall stability and degree of political polarization of the political system. Some of the other potentials of the theory are also briefly indicated.
DOI: 10.26165/juelich-data/tvwuup/ukamld
title: 225.png

description: :unav
DOI: 10.6084/m9.figshare.7075439
title: Could human coronavirus OC43 have co-evolved with early humans?

description: Abstract This paper reports on an investigation of the role of codon usage evolution on the suggested bovine-to-human spillover of Bovine coronavirus (BCoV), an enteric/respiratory virus of cattle, resulting in the emergence of the exclusively respiratory Human coronavirus OC43 (HCoV-OC43). Analyses based on full genomes of BCoV and HCoV-OC43 and on both human and bovine mRNAs sequences of cholecystokinin (CCK) and surfactant protein 1 A (SFTP1-A), representing the enteric and respiratory tract codon usage, respectively, have shown natural selection leading to optimization or deoptimization of viral codon usage to the human enteric and respiratory tracts depending on the virus genes under consideration. A higher correlation was found for the nucleotide distance at the 3rd nucleotide position of codons and codon usage optimization to the human respiratory tract when BCoV and HCoV-OC43 were compared. An MCC tree based on relative synonymous codon usage (RSCU) data integrating data from both viruses and hosts into a same analysis indicated three putative host/virus contact dates ranging from 1.54E8 to 2.44E5 years ago, suggesting that an ancestor coronavirus might have followed human evolution.
DOI: 10.26165/juelich-data/tvwuup/lc5eyf
title: 249.png

description: :unav
DOI: 10.6084/m9.figshare.7075433
title: A teenage patient with autosomal recessive polycystic kidney disease, a splenorenal shunt, and congenital hepatic fibrosis: a case report

description: ABSTRACT A 16-year-old female patient previously diagnosed with autosomal recessive polycystic kidney disease (ARPKD) presented with acute bilateral pneumonia, upper gastrointestinal bleeding caused by ruptured esophageal varices, ascites, and lower limb edema. She required intensive care and an endoscopic procedure to treat the gastrointestinal bleeding. The analysis of the differential diagnosis for chronic liver disease indicated she had a spontaneous splenorenal shunt. Ultrasound-guided biopsy revealed the patient had cirrhosis, as characteristically seen in individuals with ARPKD. She had no symptoms at discharge and was referred for review for a combined transplant.
DOI: 10.6084/m9.figshare.7075439.v1
title: Could human coronavirus OC43 have co-evolved with early humans?

description: Abstract This paper reports on an investigation of the role of codon usage evolution on the suggested bovine-to-human spillover of Bovine coronavirus (BCoV), an enteric/respiratory virus of cattle, resulting in the emergence of the exclusively respiratory Human coronavirus OC43 (HCoV-OC43). Analyses based on full genomes of BCoV and HCoV-OC43 and on both human and bovine mRNAs sequences of cholecystokinin (CCK) and surfactant protein 1 A (SFTP1-A), representing the enteric and respiratory tract codon usage, respectively, have shown natural selection leading to optimization or deoptimization of viral codon usage to the human enteric and respiratory tracts depending on the virus genes under consideration. A higher correlation was found for the nucleotide distance at the 3rd nucleotide position of codons and codon usage optimization to the human respiratory tract when BCoV and HCoV-OC43 were compared. An MCC tree based on relative synonymous codon usage (RSCU) data integrating data from both viruses and hosts into a same analysis indicated three putative host/virus contact dates ranging from 1.54E8 to 2.44E5 years ago, suggesting that an ancestor coronavirus might have followed human evolution.
DOI: 10.26165/juelich-data/tvwuup/l7ppn7
title: 081.png

description: :unav
DOI: 10.6084/m9.figshare.7075430
title: Phylogenetic relationships among Capuchin (Cebidae, Platyrrhini) lineages: An old event of sympatry explains the current distribution of Cebus and Sapajus

description: Abstract Capuchin monkeys are currently represented by four species of Cebus and eight of Sapajus. This group is taxonomically complex and several questions still need to be clarified. In the current study, using mtDNA markers and a larger sample representation than in previous studies, we seek to understand the phylogenetic relationships among the capuchin lineages and their historical biogeography. All 12 species of capuchins were analyzed for the mitochondrial Control Region and Cytochrome b to test two biogeographical hypotheses: “Reinvasion of the Amazon (ROA)” and “Sympatric Evolution (SEV)”. The phylogenetic relationships among distinct lineages within genera is consistent with an evolutionary diversification pattern probably resulting from an explosive process of diversification and dispersal between 2.0 Ma and 3.0 Ma. Also, the analyses show that the ancestral capuchins were distributed in a wide area encompassing the Amazon and Atlantic Forest. Our results support the SEV hypothesis, showing that the current syntopic distribution of Cebus and Sapajus can be explained by a sympatric speciation event in the Amazon. We also indicate that the recently proposed species taxonomy of Cebus is not supported, and that S. cay and S. macrocephalus are a junior synonym of S. apella.
DOI: 10.6084/m9.figshare.7075433.v1
title: A teenage patient with autosomal recessive polycystic kidney disease, a splenorenal shunt, and congenital hepatic fibrosis: a case report

description: ABSTRACT A 16-year-old female patient previously diagnosed with autosomal recessive polycystic kidney disease (ARPKD) presented with acute bilateral pneumonia, upper gastrointestinal bleeding caused by ruptured esophageal varices, ascites, and lower limb edema. She required intensive care and an endoscopic procedure to treat the gastrointestinal bleeding. The analysis of the differential diagnosis for chronic liver disease indicated she had a spontaneous splenorenal shunt. Ultrasound-guided biopsy revealed the patient had cirrhosis, as characteristically seen in individuals with ARPKD. She had no symptoms at discharge and was referred for review for a combined transplant.
DOI: 10.26165/juelich-data/tvwuup/gysxr2
title: 449.png

description: :unav
DOI: 10.6084/m9.figshare.7075430.v1
title: Phylogenetic relationships among Capuchin (Cebidae, Platyrrhini) lineages: An old event of sympatry explains the current distribution of Cebus and Sapajus

description: Abstract Capuchin monkeys are currently represented by four species of Cebus and eight of Sapajus. This group is taxonomically complex and several questions still need to be clarified. In the current study, using mtDNA markers and a larger sample representation than in previous studies, we seek to understand the phylogenetic relationships among the capuchin lineages and their historical biogeography. All 12 species of capuchins were analyzed for the mitochondrial Control Region and Cytochrome b to test two biogeographical hypotheses: “Reinvasion of the Amazon (ROA)” and “Sympatric Evolution (SEV)”. The phylogenetic relationships among distinct lineages within genera is consistent with an evolutionary diversification pattern probably resulting from an explosive process of diversification and dispersal between 2.0 Ma and 3.0 Ma. Also, the analyses show that the ancestral capuchins were distributed in a wide area encompassing the Amazon and Atlantic Forest. Our results support the SEV hypothesis, showing that the current syntopic distribution of Cebus and Sapajus can be explained by a sympatric speciation event in the Amazon. We also indicate that the recently proposed species taxonomy of Cebus is not supported, and that S. cay and S. macrocephalus are a junior synonym of S. apella.
DOI: 10.6084/m9.figshare.7075421
title: A Eficiência dos Juizados Especiais Estaduais Brasileiros e sua Atual Estrutura

description: Resumo O artigo avalia os níveis de eficiência e as mudanças de produtividade ao longo do tempo nos Juizados Especiais Estaduais(JEE) de cada Unidade Federativa (UF) do Brasil. A Análise Envoltória de Dados (DEA) e o Índice de Malmquist utilizados são, originariamente, determinísticos. Com o uso do Bootstrap, as metodologias passam a realizar as avaliações considerando a significância estatística dos escores de produtividade estimados. O período analisado foi 2010-2015 e o objetivo do trabalho é verificar se a atual estrutura dos Juizados Especiais Estaduais é capaz de atender à demanda pela baixa dos processos dentro do princípio da celeridade. O resultado é negativo. Considerando o último ano sob análise, mesmo sob a hipótese de plena eficiência, o número de casos pendentes chegaria a 3.502.288 no primeiro grau de jurisdição do Juizado Especial Estadual e a 304.124 casos pendentes nas Turmas Recursais. Verificase também que durante o período 2010-2015 ocorreram poucos ganhos significativos de produtividade tecnológica. Os ganhos com eficiência técnica se revelaram mais evidentes.
DOI: 10.26165/juelich-data/tvwuup/hbkyz8
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DOI: 10.6084/m9.figshare.7075421.v1
title: A Eficiência dos Juizados Especiais Estaduais Brasileiros e sua Atual Estrutura

description: Resumo O artigo avalia os níveis de eficiência e as mudanças de produtividade ao longo do tempo nos Juizados Especiais Estaduais(JEE) de cada Unidade Federativa (UF) do Brasil. A Análise Envoltória de Dados (DEA) e o Índice de Malmquist utilizados são, originariamente, determinísticos. Com o uso do Bootstrap, as metodologias passam a realizar as avaliações considerando a significância estatística dos escores de produtividade estimados. O período analisado foi 2010-2015 e o objetivo do trabalho é verificar se a atual estrutura dos Juizados Especiais Estaduais é capaz de atender à demanda pela baixa dos processos dentro do princípio da celeridade. O resultado é negativo. Considerando o último ano sob análise, mesmo sob a hipótese de plena eficiência, o número de casos pendentes chegaria a 3.502.288 no primeiro grau de jurisdição do Juizado Especial Estadual e a 304.124 casos pendentes nas Turmas Recursais. Verificase também que durante o período 2010-2015 ocorreram poucos ganhos significativos de produtividade tecnológica. Os ganhos com eficiência técnica se revelaram mais evidentes.
DOI: 10.26165/juelich-data/tvwuup/hcugfk
title: 717.png

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DOI: 10.26165/juelich-data/tvwuup/jmuv9h
title: 510.png

description: :unav
DOI: 10.6084/m9.figshare.7075415
title: Dispersion of transposable elements and multigene families: Microstructural variation in Characidium (Characiformes: Crenuchidae) genomes

description: Abstract Eukaryotic genomes consist of several repetitive DNAs, including dispersed DNA sequences that move between chromosome sites, tandem repeats of DNA sequences, and multigene families. In this study, repeated sequences isolated from the genome of Characidium gomesi were analyzed and mapped to chromosomes in Characidium zebra and specimens from two populations of C. gomesi. The sequences were transposable elements (TEs) named retroelement of Xiphophorus (Rex); multigene families of U2 small nuclear RNA (U2 snRNA); and histones H1, H3, and H4. Sequence analyses revealed that U2 snRNA contains a major portion corresponding to the Tx1-type non-LTR retrotransposon Keno, the preferential insertion sites of which are U2 snRNA sequences. All histone sequences were found to be associated with TEs. In situ localization revealed that these DNA sequences are dispersed throughout the autosomes of the species, but they are not involved in differentiation of the specific region of the W sex chromosome in C. gomesi. We discuss mechanisms of TE invasion into multigene families that lead to microstructural variation in Characidium genomes.