1,721,892 research outputs found
Evolution of a novel gene pair from a canonical toxin-antitoxin module in Escherichia coli
No full textFree-living bacteria are continuously subjected to environmental stress. This stress can be in the form of a change in temperature, pH, osmolarity or nutritional starvation. Most bacterial species contain gene modules known as Toxin-Antitoxin (TA) systems that reversibly inhibit cellular growth in response to stress; thereby helping the cells cope with a changing environment. One mechanism that bacteria have developed to combat fluctuations in environmental temperature is the cold-shock response. This response helps exponentially growing cells buffer themselves against a downshift in temperature from their optimal growing temperature; typically a shift from 37??C to 15??C for Escherichia coli (E. coli). Cold-shock proteins (Csp) are synthesized at this time. Protein Y (PY), the protein product of gene yfiA in E. coli is suggested to be a cold-shock related protein. It prevents ribosomes from dissociation during cold-shock, and in stationary phase, thereby blocking translational elongation and inhibiting cell growth. This mechanism resembled that of a typical TA system toxin. We identified a small gene, b2596, upstream of yfiA and propose that the b2596-yfiA module evolved from a true proteic TA system that functioned in cold-shock conditions; Protein X (PX), product of b2596, being the antitoxin and PY the toxin. The module still retains some of its TA system characteristics: both genes encode small proteins, have opposing charges and show sequence similarity to known TA genes. Also, like a true TA system b2596, the proposed antitoxin gene, precedes yfiA, the proposed toxin gene. However, we found that the two genes have independent transcriptional start sites. Also b2596 encodes a leaderless mRNA with UUG start and thus we predict that it cannot be translated well in vivo. PY inhibits growth of E. coli cells and functions in helping the bacterial population to survive cold-shock. Our data suggest that b2596 and yfiA have evolved from a canonical proteic TA module that was functional in cold shock. The two genes are now independent and responsive to cold shock.M.S.Includes bibliographical references (p. 56-60)
Recency is Sufficient for Reconciling Categorisation and Memory: Commentary on Devraj et al. (2024)
No full textDevraj et al. (Psychonomic Bulletin & Review. doi:10.3758/s13423-023-02448-2, 2024) argued that findings which suggest that memories for items become less accessible over time conflict with categorisation findings where exemplar performance improves across training. To reconcile this, they highlighted that under real-world conditions items tend to reappear less frequently over time, thus preferentially maintaining new items can improve performance. Typical categorisation experiments instead distribute exemplars uniformly across trials. Instead, under a power-law stimulus distribution Devraj et al. showed worsening fit for exemplar classification models across trials. They used this as evidence that forgetting behaviour adapted to task demands, reducing exemplar were accessibility and encouraging prototype use for classification decisions. By re-analysing the same data, we argue instead that this pattern can be produced with exemplar-forgetting in both conditions. By systematically increasing in the delays across which stimuli were tested, their Experimental condition exaggerated the effects of forgetting on performance in later trials compared to the Control condition. This resulted in a reversal of performance growth across trials – instead leading to a steady decline in performance. As exemplar model-fit advantage is expected to vary with performance, we suggest that trends in this advantage are not diagnostic of a shift in classification strategy. We found that a forgetting-function improved exemplar model fit to Devraj et al.’s data, and under reasonable parameters could predict the observed patterns of performance and model-fit a-priori. Compared with a strategy-shifting mixture model, exemplar-forgetting provided equivalent fits despite being more theoretically parsimonious. We suggest power-law memory decay does not produce a tension between categorisation and memory findings, as increased forgetting is found across longer retention intervals whereas the delay between exemplar learning and classification remains constant across typical categorisation experiments
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
sj-docx-2-dhj-10.1177_20552076231220804 - Supplemental material for ‘It would help people to help me’: Acceptability of digital phenotyping among young people with visual impairment and their families
No full textSupplemental material, sj-docx-2-dhj-10.1177_20552076231220804 for ‘It would help people to help me’: Acceptability of digital phenotyping among young people with visual impairment and their families by Bethany Higgins, Lee Jones, Kishan Devraj, Caroline Kilduff and Mariya Moosajee in DIGITAL HEALTH</p
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
sj-docx-1-dhj-10.1177_20552076231220804 - Supplemental material for ‘It would help people to help me’: Acceptability of digital phenotyping among young people with visual impairment and their families
No full textSupplemental material, sj-docx-1-dhj-10.1177_20552076231220804 for ‘It would help people to help me’: Acceptability of digital phenotyping among young people with visual impairment and their families by Bethany Higgins, Lee Jones, Kishan Devraj, Caroline Kilduff and Mariya Moosajee in DIGITAL HEALTH</p
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