1,721,008 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
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
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Beyond the Model and Into the Map: A Protein Abstract
Get PDFProteins populate structural ensembles. Defining these ensembles and understanding the role of the interconversions between structures is a grand challenge of structural biology. My work addresses that challenge through the development and application of new methods to reveal sparsely populated structures. Quantitative electron-density map interpretation, implemented in Ringer, provides an objective, systematic method to identify previously undiscovered alternate side chain substates that mediate conformational transitions in proteins. Next, I applied these methods to study the role of the interconversions of an enzyme, the human proline isomerase CypA, between two conformations during its catalytic cycle. Using the dual strategies of ambient-temperature X-ray crystallographic data collection and automated electron-density sampling, I defined the previously undiscovered minor state as a network of alternate side chain conformations. A conservative mutation outside the active site inverts the equilibrium between the substates and causes large, parallel reductions in the conformational interconversion rates and the catalytic rate. The temperature dependent differences in electron density observed with CypA led me to critically examine the assumption that crystal freezing does not significantly bias protein structure. I found extensive remodeling of the crystal lattice upon freezing. Crystal freezing also leads to improved packing through reduction of small voids and a reduction in protein volume. I used real-space electron density sampling to show that these voids can be transiently populated by alternate conformations in the room temperature ensemble. This work shows how crystal freezing biases our understanding of protein packing and can lead to differences in the spatial distribution of the dynamic features of protein side chains. These studies highlight the importance of conformational diversity in protein function. By looking beyond the model and into the map, we can find that polysteric regions often populate conformations that resemble the structures populated along reaction or evolutionary trajectories. Thus, understanding polysterism yields insights into where a protein might visit during its reaction cycle and where it has been during its evolution
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Peptidoglycan Degrading and Sensing Systems of Mycobacterium tuberculosis
Get PDFMycobacterium tuberculosis (Mtb) cell wall, built on a cross-linked sugar-peptide polymer called peptidoglycan, protects the bacterial cell from adverse environments. Peptidoglycan homeostasis is maintained by extracellular peptidoglycan synthases and hydrolases. Intricate coordination of their activities is required to maintain structural integrity of the cell wall during growth, division, and response to stress. The sensor protein kinase B (PknB) is likely to play a critical role in monitoring the state of the peptidoglycan outside the cell and inducing subsequent metabolic changes inside. In this study, computational, biochemical, and structural approaches were used to characterize the peptidoglycan hydrolases of Mtb and to investigate the molecular mechanism of peptidoglycan signaling through PknB.Peptidoglycan hydrolases are critical players in bacterial growth, division, cell shape determination, and peptidoglycan fragment-mediated communication. Computational analysis identified 22 mycobacterial peptidoglycan hydrolases based on homology to known enzymes from model organisms. The peptidoglycan degradation machinery of Mtb includes 4 N-acetylmuramoyl-L-alanine amidases, 8 lytic transglycosidases, and 10 peptidases of various specificities. Ten of these enzymes form a core set of mycobacterial peptidoglycan hydrolases, while four of them are essential for growth in Mtb. Comprehensive biochemical and structural investigation of the Mtb peptidoglycan hydrolases was initiated by cloning and heterologously expressing constructs representing all 22 Mtb peptidoglycan hydrolases in Escherichia coli. Robust expression was observed for all but one target protein. Twelve were successfully purified on large scale.The peptidoglycan amidases Rv3717 and Rv3915 share similar catalytic cores yet have non-redundant functions in peptidoglycan turnover. Hydrolase activity assays using polymerized peptidoglycan sacculi and soluble peptidoglycan fragments elucidated contributions of individual amino acid residues, metal binding, and disulfide bond formation to catalysis. The structure of product-bound Rv3717 suggested a mechanism that limits this enzyme's activity on polymerized sacculi.Peptidoglycan D,D-peptidases Rv2911, Rv3330 and Rv3627 are low molecular weight penicillin-binding proteins that participate in peptidoglycan maturation and degradation. Surprisingly, these three enzymes were inactive on peptidoglycan sacculi or peptidoglycan fragments, yet were active on beta-lactams meropenem and Bocillin. The structure of Rv3330 solved in complex with meropenem revealed a potential peptide-binging groove distant from the active site. The observed lack of activity of low molecular weight penicillin-binding proteins suggests a requirement for an activator. Discovery of such factors will significantly advance our understanding of Mtb peptidoglycan homeostasis.PknB is an essential sensor kinase that controls cell wall biosynthesis. Its homologs in Gram-positive bacteria have been implicated in binding peptidoglycan fragments and in mediating bacterial responses to cell wall stress. To investigate the mechanism of peptidoglycan recognition by PknB, the structure of its extracellular sensor domain was solved. It consists of four 70-amino acid PASTA repeat domains that adopt an extended conformation. The last repeat domain contains a hydrophobic pocket with a conserved tryptophan, a signature of a ligand-binding site. The structure of PknB extracellular domain suggests that ligand-dependent localization and oligomerization control kinase activity
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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Mechanisms of Mycobacterium tuberculosis Serine/Threonine Protein Kinase Activation
Get PDFMycobacterium tuberculosis (Mtb) coordinates a wide variety of metabolic and cellular responses to changing external environments throughout the multiple stages of infection. Signaling kinases are critical for these responses. The Mtb genome encodes 11 Serine/Threonine Protein Kinases (STPKs) that function as important nodes of this sensing and response network, but the chemical and structural changes that mediate kinase activation have not been elucidated. Autophosphorylation activates several of the Mtb STPKs, and kinase dimerization can activate receptor kinases for autophosphorylation through an allosteric dimer interface. Inter-kinase phosphorylation has been reported, but the function and specificity of these interactions remain unknown. In this study, a biochemical approach was used to comprehensively map the cross-kinase trans-phosphorylation activity of the Mtb STPKs. The results reveal a pattern of kinase interactions that suggests each protein plays a distinct regulatory role in controlling cellular processes by phosphorylating other kinases. The PknB and PknH STPKs act in vitro as master regulators that are activated only through autophosphorylation and also phosphorylate other STPKs. In contrast, the signal-transduction kinases PknE, PknJ and PknL are phosphorylated by the master regulatory STPKs and phosphorylate other kinases. The substrate STPKs PknA, PknD, PknF and PknK are phosphorylated by upstream STPKs, but do not phosphorylate other kinases. The delineation of the Mtb STPK signaling networks reveals for the first time the specific network of STPK phosphorylation that may mediate the intracellular signaling circuitry. STPKS are activated and inhibited by phosphorylation at different residues. The regulatory role of the extensive Mtb STPK trans-phosphorylation network is unknown. Through mass spectrophotometry and mutagenesis, the amino acids targeted by each phosphorylation were identified. I find that key activation loop residues are the targets of both autophosphorylation and trans-phosphorylation. Mutation of the two conserved threonines in the activation loops of nine Mtb STPKs renders the kinases inactive. These results demonstrate that activation loop phosphorylation is a common mechanism of Mtb STPK activation. To explore the structural implications of activation loop phosphorylation, I determined the crystal structures of the phosphorylated and unphosphorylated Mtb PknH kinase domain. The PknH kinase domain forms a back-to-back dimer observed previously in the structures of Mtb PknB and PknE. Amino-acid substitutions in the dimer interface fail to block kinase dimerization or autophosphorylation. Unexpectedly, the PknH activation loop is folded in the unphosphorylated form and disordered in the active, phosphorylated enzyme. These structures revealed that the back-to-back kinase dimer is a surprisingly stable structure that does not undergo global conformational changes with phosphorylation or nucleotide binding. Unlike the well-established, conformational regulatory mechanisms of eukaryotic STPKs, PknH activation may be a biochemical process mediated by changes in nucleotide affinity or activation loop disorder rather than remodeling of the overall kinase-domain architecture. To establish the effects of stepwise phosphorylation of an Mtb STPK, I determined the structures of the PknK kinase domain modified with 0, 1, or multiple phosphoryl groups. PknK is one of the two solution STPKs in Mtb and is phosphorylated by multiple upstream kinases. Mass spectrophotometry revealed that the trans-phosphorylation and autophosphorylation reactions resulted in varying numbers of phosphate groups on this substrate protein. Crystal structures revealed that, like PknH, PknK does not undergo conformational remodeling following activation loop phosphorylation. Unlike many eukaryotic homologs, the unphosphorylated forms of PknH and PknK bind ATP analogs. These two examples suggest that phosphorylation activates the Mtb STPKs by directly changing the properties of the activation loop. Based on these results, I propose the testable new idea that activation loop phosphorylation may regulate the Mtb STPKs by directly changing the affinities for protein substrates or nucleotides. The absence of conformational remodeling of PknH and PknK upon activation loop phosphorylation implies that the prokaryotic and eukaryotic STPKs are regulated by different mechanisms
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