1,720,997 research outputs found
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Suspension cell culture as a tool for secondary cell wall studies in C4 grasses
No full textAs características físico-químicas da parede celular constituem um grande gargalo na obtenção dos açúcares fermentáveis a partir dos polissacarídeos de parede celular presentes na biomassa, fato conhecido como recalcitrância da biomassa vegetal. A utilização da biomassa na produção de biocombustíveis requer um melhor entendimento sobre os mecanismos que permeiam os processos de deposição de parede celular e metabolismo de lignina. Nesse contexto, a maior parte do conhecimento foi gerado em espécies eudicotiledôneas, havendo uma significativa lacuna para gramíneas, apesar do seu grande potencial para acúmulo de biomassa. Portanto, há uma necessidade de se estabelecer ferramentas-modelos que permitam elucidar características exclusivas da parede celular secundária de gramíneas C4, cujo conhecimento não pode ser extrapolado a partir de eudicotiledôneas. O presente trabalho propôs estabelecer um sistema de células em suspensão como ferramenta-modelo em estudos sobre parede celular secundária em gramíneas C4. Para tal, três espécies foram inclusas: Sorghum bicolor, Setaria viridis e cana-de-açúcar. Devido às características recalcitrantes do sorgo, apenas as suspensões celulares de S. viridis e cana-de-açúcar foram estabelecidas. Subsequentemente, estas culturas foram utilizadas na tentativa de se desenvolver duas aplicações para o estudo de parede secundária: i) culturas xilogênicas, em que as células em suspensão são induzidas a se transdiferenciar em elementos traqueais; e ii) sistema de protoplastos para ensaios de transativação para testar o potencial papel de fatores de transcrição na regulação transcricional da deposição de parede celular. Somente as culturas de cana-de-açúcar responderam aos tratamentos testados para indução da transdiferenciação de elementos traqueais, baseados em protocolos estabelecidos para outras gramíneas. Análises de expressão gênica por RT-qPCR foram utilizadas para caracterizar a variação da expressão de genes-alvo durante este processo. Ademais, as paredes celulares das células em suspensão de cana-de-açúcar foram digeridas com um coquetel de hidrolases para a produção de protoplastos. A cultura de células em suspensão de cana-de-açúcar e suas aplicações aqui estabelecidas poderão ser utilizadas na elucidação de aspectos únicos do processo de deposição de parede celular secundária em gramíneas C4The physicochemical features of the cell wall represent a major bottleneck for the processing of cell wall polysaccharides present in biomass into fermentable sugars, a fact known as plant biomass recalcitrance. Biofuels production from biomass requires a better understanding on the molecular mechanisms underlying secondary cell wall deposition and lignin metabolism. In this context, most of the current knowledge has been generated in eudicots species, whereas significantly less is known for grasses, despite of their great potential for biomass accumulation. Therefore, the development of tools that allow the discovery of specific aspects of C4 grasses secondary cell walls is of great interest, because this knowledge cannot be extrapolated from data generated for eudicots. In the present work, we aimed to develop suspension cell cultures as a tool for the study of secondary cell wall metabolism in C4 grasses. For this purpose, three species were employed: Sorghum bicolor, Setaria viridis and sugarcane. Because of the recalcitrant nature of sorghum, only suspensions cells of S. viridis and sugarcane were successfully established. Subsequently, these cultures were used in an attempt to develop two applications to study secondary cell walls: i) xylogenic cultures, in which the suspension cells are induced to transdifferentiate into tracheary elements; and ii) a protoplast system to be used in transactivation assays to test the potential role of transcriptional factors in the regulation of secondary wall deposition. Only the suspension cultures of sugarcane showed a positive response to the tested treatments for the induction of tracheary elements formation, which were based on modifications of previous protocols established for other grasses. Gene expression analysis by RT-qPCR was used to characterize the variation of the expression of target genes during this process. Moreover, the cell walls of sugarcane suspension cells were digested with a cocktail of hydrolases to produce protoplasts, which were used in transactivation assays between transcriptional factors known to be involved in secondary cell wall deposition and their putative target genes, as a proof-of-concept. The sugarcane suspension cells and their applications established in this work might be used to further elucidate unique aspects of secondary cell wall deposition in C4 grasse
Caffeoyl Shikimate Esterase (CSE): the missing link between the metabolism of chlorogenic acids and lignin?
Get PDFÁcidos clorogênicos (CGAs) e lignina são produtos da via dos fenilpropanóides. Enquanto o primeiro está associado à respostas das plantas a estresses, o segundo é um biopolímero depositado nas paredes secundárias e responsável pela sustentação estrutural da planta e impermeabilização dos vasos do xilema, garantindo o transporte de água. Visto que a estrutura de CGAs é quimicamente semelhante àquela de alguns intermediários da via biossintética de lignina e visto que CGAs podem ser convertidos de volta à hidroxicinamoil- CoAs in vitro, estes compostos tem sido considerados autênticos intermediários para a produção de lignina. No entanto, ainda não está claro se CGAs são de fato remobilizados para a produção de monômeros de lignina ao longo do desenvolvimento ou em resposta a sinais ambientais. A recente descoberta que caffeoyl shikimate esterase (CSE) é uma enzima central para a biossíntese de lignina abre uma nova possibilidade de explorar a potencial interdependência entre os metabolismos de CGAs e lignina. Considerando que i) o substrato de CSE, cafeoil chiquimato (via de lignina), é estruturalmente muito similar ao cafeoil quinato (CGA); ii) que CSE recombinante de Arabidopsis é capaz de utilizar não somente cafeoil chiquimato mas também outros ésteres como substratos in vitro; e iii) que o silenciamento de CSE em álamo resultou no acúmulo de CGAs nas linhagens transgênicas, a hipótese deste trabalho é que CSE também é capaz de utilizar CGAs como substrato e, consequentemente, estaria envolvida no metabolismo de CGAs. Assim, o objetivo deste trabalho foi realizar um estudo funcional de CSE em batata (Solanum tuberosum), uma Solanaceae que acumula altos níveis de CGAs. Buscas por BLASTp seguidas de análises filogenéticas demonstraram que StCSE ocorre como gene único no genoma de batata, similar a outras espécies com genoma diploide. Análises transcriptômicas in silico e por RT-qPCR em diferentes tecidos de batata revelaram uma correlação positiva entre os padrões de expressão de StCSE e StHCT, um gene biossintético de lignina, enquanto uma correlação negativa foi observada para StCSE x StHQT, um gene biossintético de CGAs. StCSE recombinante foi produzida em Escherichia coli e purificada utilizando cromatografia por afinidade para a realização de ensaios enzimáticos in vitro com três substratos: cafeoil chiquimato, cafeoil quinato (um CGA monoéster) e 3,5-dicafeoil quinato (um CGA di-éster). Esses ensaios mostraram que StCSE não somente é capaz de utilizar CGAs como substrato in vitro mas que estes fenólicos são utilizados com maior eficiência do que o próprio cafeoil chiquimato. Esses resultados sugerem que CSE é uma enzima envolvida tanto no metabolismo de lignina quanto no metabolismo de CGAs, potencialmente atuando na mobilização de CGAs para a síntese de monômeros de lignina e/ou outros fenilpropanóides.Chlorogenic acids (CGAs) and lignins are products of the phenylpropanoid pathway. While the first is associated with plant responses to stress, the second is a biopolymer deposited in the secondary walls and responsible for the structural support of the plant and waterproofing the xylem vessels, ensuring water transport. Since the structure of CGAs is chemically similar to that of some intermediates of the lignin biosynthetic pathway and since CGAs can be converted back to hydroxycinnamoyl-CoAs in vitro, these compounds have been considered authentic intermediates for lignin production. However, it remains unclear whether CGAs are indeed remobilized for the production of lignin monomers throughout development or in response to environmental cues. The recent discovery that caffeoyl shikimate esterase (CSE) is a central enzyme for lignin biosynthesis opens a new possibility to explore the potential interdependence between the metabolisms of CGAs and lignin. Considering that i) the CSE substrate, caffeoyl shikimate (lignin pathway), is structurally very similar to caffeoyl quinate (CGA); ii) that recombinant CSE from Arabidopsis is capable of using not only caffeoyl shikimate but also other esters as substrates in vitro; and iii) that the silencing of CSE in poplar resulted in the accumulation of CGAs in transgenic lines, the hypothesis of this work is that CSE is also capable of using CGAs as a substrate and, consequently, would be involved in the metabolism of CGAs. Therefore, the aim of this work was to perform a functional study of CSE in potato (Solanum tuberosum), a Solanaceous species that accumulates high levels of CGAs. BLASTp searches followed by phylogenetic analyzes revealed that StCSE occurs as a single gene in the potato genome, similar to other species with a diploid genome. In silico and RT-qPCR transcriptomic analyzes using different potato tissues revealed a positive correlation between the expression patterns of StCSE and StHCT, a lignin biosynthetic gene, whereas a negative correlação was observed for StCSE x StHQT, a CGA biosynthetic gene. Recombinant StCSE was produced in Escherichia coli and purified using affinity chromatography to perform in vitro enzymatic assays with three substrates: caffeoyl shikimate, caffeoyl quinate (a CGA monoester) and 3,5-dicaffeoyl quinate (a CGA di-ester). These assays demonstrated that StCSE is not only capable of using CGAs as a substrate in vitro, but that these phenolics are used more efficiently than caffeoyl shikimate. These results suggest that CSE is an enzyme involved in both lignin metabolism and CGA metabolism, potentially in the mobilization of CGAs toward the synthesis of lignin monomers and/or other phenylpropanoids
Identification of laccases and class III peroxidases potentially involved in the lignification in Setaria viridis (L.) P.Beauv.
Get PDFAs lacases e peroxidases de classe III são enzimas essenciais no processo de polimerização da lignina, compreendendo uma etapa crucial na biossíntese de lignina e formação das paredes celulares secundárias em espécies vegetais. Estas enzimas estão envolvidas na oxidação dos monolignóis, sendo responsáveis pela formação dos radicais antes de sua incorporação no polímero de lignina. Ambas pertencem a grandes famílias enzimáticas multigênicas, apresentando membros funcionalmente caracterizados com papel na polimerização de lignina e outros ainda não caracterizados ou apontados com função direta no metabolismo da lignina. Neste trabalho, foi realizada uma caracterização abrangente das famílias de genes de lacase e peroxidase de classe III em S. viridis, para identificar os membros potencialmente envolvidos na polimerização da lignina. Foram identificados 52 genes codificadores de lacases (SvLAC1 a SvLAC52) e 154 genes codificadores de peroxidases de classe III (SvPRX1 a SvPRX154) no genoma de S. viridis. Em ambas as famílias, a expansão do número de genes foi em grande parte resultado de eventos de duplicação em tandem. Cinco genes de lacase (SvLAC9, SvLAC13, SvLAC15, SvLAC50 e SvLAC52) e cinco genes de peroxidase (SvPRX49, SvPRX58, SvPRX119, SvPRX122 e SvPRX149) foram identificados como fortes candidatos a desempenhar um papel na lignificação. Esses genes foram selecionados com base em critérios como proximidade filogenética com genes de lignina previamente caracterizados em outras espécies, padrões de expressão similares aos observados em genes biossintéticos de lignina no entrenó em elongação de S. viridis, e alta expressão em tecidos de S. viridis submetidos à lignificação ativa. Além disso, a presença de elementos cis relacionados à parede celular secundária nas regiões promotoras desses genes sugere que sua expressão é regulada pelas mesmas redes que controlam a deposição de lignina. Experimentos de hibridização in situ confirmaram que os genes selecionados são expressos em células com lignificação ativa, com lacases e peroxidases mostrando diferentes especificidades teciduais, sugerindo possíveis eventos de subfuncionalização dentro dessas famílias enzimáticas. Particularmente, o gene SvPRX58 se destacou entre as peroxidases por conter todos os motivos estruturais característicos das peroxidases de siringil (S), sugerindo que esta enzima pode oxidar o álcool sinapílico, um monolignol específico. A identificação desses genes de lacase e peroxidase em S. viridis fornece novos insights sobre os mecanismos moleculares envolvidos na lignificação e oferece potenciais alvos para estratégias de bioengenharia visando à modificação da lignina, com aplicações promissoras para a bioeconomia.Lignin biosynthesis and secondary cell wall formation are critical processes in plant species, driven by the activity of key enzymes such as laccases and class III peroxidases. These enzymes facilitate the oxidation of monolignols, forming radicals that are subsequently incorporated into the lignin polymer. Laccases and peroxidases belong to large multigene families, with some members characterized for their role in lignin polymerization, while others remain uncharacterized or indirectly linked to lignin metabolism. This study provides a comprehensive characterization of the laccase and class III peroxidase gene families in Setaria viridis (S. viridis) to identify members potentially involved in lignin polymerization. A total of 52 laccase genes (SvLAC1 to SvLAC52) and 154 class III peroxidase genes (SvPRX1 to SvPRX154) were identified in the S. viridis genome, with gene family expansions primarily resulting from tandem duplication events. Five laccase genes (SvLAC9, SvLAC13, SvLAC15, SvLAC50, and SvLAC52) and five peroxidase genes (SvPRX49, SvPRX58, SvPRX119, SvPRX122, and SvPRX149) were identified as strong candidates for roles in lignification. Selection criteria included phylogenetic proximity to previously characterized lignin genes in other species, expression patterns resembling lignin biosynthetic genes during internode elongation, and high expression in tissues undergoing active lignification. The presence of secondary cell wall-related cis-elements in the promoter regions of these genes suggests regulation by networks controlling lignin deposition. In situ hybridization experiments confirmed expression in cells with active lignification, with laccases and peroxidases displaying distinct tissue specificities, hinting at possible subfunctionalization events within these enzyme families. Notably, SvPRX58, among the peroxidases, possesses structural motifs characteristic of syringyl (S) peroxidases, indicating a potential role in the oxidation of sinapyl alcohol, a specific monolignol. The identification of these laccase and peroxidase genes in S. viridis offers new insights into the molecular mechanisms underlying lignification and presents potential targets for bioengineering strategies aimed at lignin modification, with promising applications in the bioeconomy
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
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