1,721,358 research outputs found
Research
No full textBackground: DIALIGN-T is a reimplementation of the multiple-alignment program DIALIGN. Due to several algorithmic improvements, it produces significantly better alignments on locally and globally related sequence sets than previous versions of DIALIGN. However, like the original implementation of the program, DIALIGN-T uses a a straight-forward greedy approach to assemble multiple alignments from local pairwise sequence similarities. Such greedy approaches may be vulnerable to spurious random similarities and can therefore lead to suboptimal results. In this paper, we present DIALIGN-TX, a substantial improvement of DIALIGN-T that combines our previous greedy algorithm with a progressive alignment approach. Results: Our new heuristic produces significantly better alignments, especially on globally related sequences, without increasing the CPU time and memory consumption exceedingly. The new method is based on a guide tree; to detect possible spurious sequence similarities, it employs a vertex-cover approximation on a conflict graph. We performed benchmarking tests on a large set of nucleic acid and protein sequences For protein benchmarks we used the benchmark database BALIBASE 3 and an updated release of the database IRMBASE 2 for assessing the quality on globally and locally related sequences, respectively. For alignment of nucleic acid sequences, we used BRAliBase II for global alignment and a newly developed database of locally related sequences called DIRM-BASE 1. IRMBASE 2 and DIRMBASE 1 are constructed by implanting highly conserved motives at random positions in long unalignable sequences. Conclusion: On BALIBASE3, our new program performs significantly better than the previous program DIALIGN-T and outperforms the popular global aligner CLUSTAL W, though it is still outperformed by programs that focus on global alignment like MAFFT, MUSCLE and T-COFFEE. On the locally related test sets in IRMBASE 2 and DIRM-BASE 1, our method outperforms all other programs while MAFFT E-INSi is the only method that comes close to the performance of DIALIGN-TX
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
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
Graph Product Structure for -Framed Graphs
No full textGraph product structure theory expresses certain graphs as subgraphs of the strong product of much simpler graphs. In particular, an elegant formulation states that every planar graph is a subgraph of the strong product of a path and of a bounded treewidth graph. Such formulations allow to lift combinatorial results for bounded treewidth graphs to graph classes for which the product structure holds, such as to planar graphs [Dujmović et al., J. ACM, 67(4), 22:1-38, 2020]. In this paper, we join the search for extensions of this powerful tool beyond planarity by considering the h-framed graphs, a graph class that includes 1-planar, optimal 2-planar, and k-map graphs (for appropriate values of h). We establish a graph product structure theorem for h-framed graphs stating that the graphs in this class are subgraphs of the strong product of a path, of a planar graph of treewidth at most 3, and of a clique of size 3⌊h2⌋+⌊ h3 ⌋ − 1. This allows us to improve over the previous structural theorems for 1-planar and k-map graphs. Our results lead to significant progress over the previous bounds on the queue number, non-repetitive chromatic number, and p-centered chromatic number of these graph classes, e.g., we lower the currently best upper bound on the queue number of 1-planar graphs and k-map graphs from 115 to 82 and from ⌊332(k+ 3⌊ k2 ⌋ − 3)⌋ to ⌊332(3⌊ k2⌋+⌊ k3 ⌋ − 1)⌋, respectively. We also employ the product structure machinery to improve the current upper bounds on the twin-width of 1-planar graphs from O(1) to 72. All our structural results are constructive and yield efficient algorithms to obtain the corresponding decompositions
Vertex angle and crossing angle resolution of leveled tree drawings
No full textWe study the problem of computing leveled tree drawings, i.e., straight-line drawings of trees where the vertices have distinct preassigned y-coordinates. Our optimization goal is to maximize the crossing angle resolution (i.e., the minimum angle formed by any two crossing edges) and/or the vertex angle resolution (i.e., the minimum angle formed by two edges incident to the same vertex) of the drawing. We provide tight and almost tight worst case bounds for the crossing angle resolution and for the total angle resolution (i.e., the minimum of crossing and vertex angle resolution), respectively
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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