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Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe 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
Expression of RuBP carboxylase small subunit genes involves sequences with enhancer-like properties
No full textChimaeric genes encoding chloramphenicol acetyltransferase (CAT) under the control of promoter fragments of varied length from a pea RuBP carboxylase small subunit gene were introduced into tobacco cells by Agrobacterium-mediated cell transformation and their expression characteristics studied in calli grown in light or darkness. These deletion studies demonstrated that nucleotide sequences at least 722 bp 5' to the mRNA cap site are required for high levels of light-inducible expression, although sequences residing within 92 bp of the cap site are still capable of directing low levels of photoregulated expression. Similar to transcriptional enhancer elements described in animal viral and cellular systems, nucleotide sequences involved in directing photoregulated expression act independent of orientation with either homologous or heterologous transcriptional control signals
Variations on the Author
Full text link“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
Full text linkWe 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
Transposable elements contribute to activation of maize genes in response to abiotic stress.
Full text linkTransposable elements (TEs) account for a large portion of the genome in many eukaryotic species. Despite their reputation as "junk" DNA or genomic parasites deleterious for the host, TEs have complex interactions with host genes and the potential to contribute to regulatory variation in gene expression. It has been hypothesized that TEs and genes they insert near may be transcriptionally activated in response to stress conditions. The maize genome, with many different types of TEs interspersed with genes, provides an ideal system to study the genome-wide influence of TEs on gene regulation. To analyze the magnitude of the TE effect on gene expression response to environmental changes, we profiled gene and TE transcript levels in maize seedlings exposed to a number of abiotic stresses. Many genes exhibit up- or down-regulation in response to these stress conditions. The analysis of TE families inserted within upstream regions of up-regulated genes revealed that between four and nine different TE families are associated with up-regulated gene expression in each of these stress conditions, affecting up to 20% of the genes up-regulated in response to abiotic stress, and as many as 33% of genes that are only expressed in response to stress. Expression of many of these same TE families also responds to the same stress conditions. The analysis of the stress-induced transcripts and proximity of the transposon to the gene suggests that these TEs may provide local enhancer activities that stimulate stress-responsive gene expression. Our data on allelic variation for insertions of several of these TEs show strong correlation between the presence of TE insertions and stress-responsive up-regulation of gene expression. Our findings suggest that TEs provide an important source of allelic regulatory variation in gene response to abiotic stress in maize
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe 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
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Interactions among gene regulation and expression, sequence deletion, and purifying selection following whole genome duplications in flowering plants
Full text linkPolyploidy, or whole genome duplication, is rampant among both extant and ancient flowering plant species. Whole genome duplications create simultaneous copies of all genes contained within a genome as well as associated regulatory sequences. These duplication and the subsequent deletions of redundant coding and noncoding sequence both shape the natural evolution of plant genomes and provide a unique opportunity for researchers to characterize the regulatory sequences which determine when, in which cells and in what quantities the mRNA encoded for by particular genes will be produced. This dissertation describes a model for explaining both bias in gene loss between parental subgenomes and the escape from preferential retention of duplicated genes between sequential whole genome duplications. Bias in gene deletion between individual duplicated segments had been previously observed by the publication of the sorghum and maize genomes provided an opportunity to demonstrate this bias was a consistent mark distinguishing whole pairs of ancestral chromosomes, and that ongoing gene loss remains consistently biased between high and low gene loss subgenomes millions of generations after a whole genome duplication. Bias in both ancestral and ongoing gene loss is shown to be correlated with biased gene expression between parental subgenomes with genes on the low gene loss subgenome tending to show higher expression levels than duplicate copies of the same genes on the high gene loss subgenome. This phenomena, originally referred to as genome dominance, although the literature has since become somewhat confused, provides an explanation both for biased gene loss between parental subgenomes and for the escape of deletion-resistant genes from the ratchet of ever increasing copy numbers through continued whole genome duplications. This dissertation also demonstrates the use of polyploid lineage - in this case maize - as a deletion machine to rapidly characterize the function of regulatory sequences shared by orthologous genes within a clade. It was possible to develop testable hypothesis about the specific function of individual regulatory sequences by combining conserved noncoding sequence sequence datasets, noncoding sequence deletions identified using comparative genomics with analysis and visualization of gene expression data from diverse organs, tissues, and cell types. As a test of the accuracy of this method, a putative pollen specific enhancer of expression identified using expression data from maize was cloned from the orthologous sorghum gene and used to drive the expression of a reporter construct in Brachypodium distachyon. Polyploid deletion machines have the potential to radically accelerate the characterization of noncoding regulatory sequences, an area of genetics previously largely untouched by advances next generation sequencing technologies
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Elucidating the impacts of environment and host on the assembly of plant-associated microbial communities
Full text linkThe microbial world is integrally involved with major ecological processes and affects all domains of life. With the numerous societal challenges we face today, efforts are being directed towards better utilizing microbial communities to support host health and resilience. In regards to agriculture, this includes the fortification of crop production through microbial amendments and microbiome manipulation. To better engineer microbiomes capable of promoting plant growth and ameliorating stress, additional research is needed to untangle the relative contributions of environmental and host factors in recruiting and maintaining beneficial microbes, while repelling potential pathogens. The work presented here seeks to identify and explore the importance of a set of these environmental and host forces in shaping the root and rhizosphere microbiomes of crop species. Specifically, the impacts of disturbance on plant-microbe interactions are characterized in relation to the farming practices of tillage and cover-cropping, heat and drought stress, and host evolution.This research first explores how a set of widely employed agricultural soil management practices influence the belowground interactions between sorghum, bacteria, and fungi. Currently, it is not well characterized how cultivation systems influence microbiome assembly and activity. Utilizing next generation sequencing methods, we characterized a field system managed for close to two decades with standard tillage or no till practices in combination with either cover-cropping or letting the field lay fallow. We observed a promotion of microbial diversity by standard till and determined that fungal communities responded to a greater degree - in both composition and activity - to management practice than bacteria. Interestingly, despite distinct communities under each regime, similar plant growth outcomes were observed. This work informs understandings of how intermittent soil disturbance impacts agroecosystems and highlights the importance of cross-kingdom analyses.This work then investigates the combined and isolated impacts of heat and drought stress on sorghum microbiome assembly. Recent studies of drought and the plant microbiome have shown a high degree of variability in bacterial enrichment under drought, particularly for the phylum Actinobacteria. As heat often co-occurs with drought in the field, we sought to determine the relative contributions of temperature to this enrichment. Using a set of controlled growth chamber experiments, we observed that high temperatures do indeed correlate to a restructuring of sorghum-associated bacterial communities. This community differed from what was observed under drought alone, and the majority of indicator taxa within Actinobacteria were not shared between stresses. These results further our knowledge on how different abiotic stresses help modulate community interactions and lay the foundation for additional work characterizing the mechanisms involved in differential microbial enrichment.In the final chapter of this work, the influence of host evolution on the associations between plants and their belowground microbiome is explored. Past research has shown that plant domestication and polyploidy can broadly influence plant biotic and abiotic interactions. We utilized three approaches - two field studies and one greenhouse-based experiment - to determine whether patterns in bacterial community assembly in wheat roots and rhizospheres could be partially attributable to these host factors. Collectively, we found little evidence of ploidy level and domestication status correlating with shifts in wheat bacterial communities. However, the greatest influence of the host on the microbiome appeared to occur in the rhizosphere compartment, and we suggest future work focuses on this environment to further characterize how host genomic and phenotypic changes influence plant-microbe communications. This research informs perspectives on what key driving forces may underlie microbiome structuring, as well as where future efforts may be best directed towards fortifying plant growth by microbial means.Taken together, this work addresses fundamental gaps in our knowledge of the plant microbiome and the factors that help govern its structure and function. It demonstrates the ecological importance of agricultural soil management practices on plant-microbial interactions, uncovers the distinct roles of heat and drought stress in plant microbiome assembly, and indicates that domestication and polyploidy are minor contributors in shaping the wheat bacterial microbiome
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