31,326 research outputs found
Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins.
No full textBackground: large datasets of protein interactions provide a rich resource for the discovery of Short Linear Motifs (SLiMs) that recur in unrelated proteins. However, existing methods for estimating the probability of motif recurrence may be biased by the size and composition of the search dataset, such that p-value estimates from different datasets, or from motifs containing different numbers of non-wildcard positions, are not strictly comparable. Here, we develop more exact methods and explore the potential biases of computationally efficient approximations. Results: a widely used heuristic for the calculation of motif over-representation approximates motif probability by assuming that all proteins have the same length and composition. We introduce pv, which calculates the probability exactly. Secondly, the recently introduced SLiMFinder statistic Sig, accounts for multiple testing (across all possible motifs) in motif discovery. However, it approximates the probability of all other possible motifs, occurring with a score of p or less, as being equal to p. Here, we show that the exhaustive calculation of the probability of all possible motif occurrences that are as rare or rarer than the motif of interest, Sig', may be carried out efficiently by grouping motifs of a common probability (i.e. those which have permuted orders of the same residues). Sig'v, which corrects both approximations, is shown to be uniformly distributed in a random dataset when searching for non-ambiguous motifs, indicating that it is a robust significance measure. Conclusions: a method is presented to compute exactly the true probability of a non-ambiguous short protein sequence motif, and the utility of an approximate approach for novel motif discovery across a large number of datasets is demonstrated
Variations on the Author
No full text“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
The relation between questions indicating transient ischaemic attack and stroke in 20 years of follow up in men and women in the Renfrew/Paisley Study
No full text<b>STUDY OBJECTIVE</b> Transient ischaemic attack (TIA) is often a precursor to stroke, so identification of people experiencing TIA could assist in stroke prevention by indicating those at high risk of stroke who would benefit most from intervention for other stroke risk factors. The objective of this study was to investigate whether answers to a simple questionnaire for TIA could predict the occurrence of stroke in the following 20 years.
DESIGNProspective cohort study, conducted between 1972 and 1976, with 20 years of follow up.
<b>SETTING</b> Renfrew and Paisley, Scotland.
<b>PARTICIPANTS</b> 7052 men and 8354 women aged 45-64 years at the time of screening completed a questionnaire and attended a physical examination. The questionnaire asked participants if they had ever, without warning, suddenly lost the power of an arm, suddenly lost the power of a leg, suddenly been unable to speak properly or suddenly lost consciousness. These four questions were taken as indicators of TIA and were related to subsequent stroke mortality or hospital admission.
<b>MAIN RESULTS</b> For women, each question was significantly related to stroke risk, whereas for men only the question on loss of power of arm was significantly related to stroke risk. Men and women answering two or more questions positively had double the relative rate of stroke compared with men and women answering none of the questions positively, even after adjusting for other risk factors for stroke.
<b>CONCLUSIONS</b> A simple questionnaire for TIA could help predict stroke over 20 years of follow up. Targeting men and women who report TIA with early treatment could help to prevent strokes from occurring
Computational identification and analysis of protein short linear motifs
No full textShort linear motifs (SLiMs) in proteins can act as targets for proteolytic cleavage, sites of post-translational modification, determinants of sub-cellular localization, and mediators of protein-protein interactions. Computational discovery of SLiMs involves assembling a group of proteins postulated to share a potential motif, masking out residues less likely to contain such a motif, down-weighting shared motifs arising through common evolutionary descent, and calculation of statistical probabilities allowing for the multiple testing of all possible motifs. Much of the challenge for motif discovery lies in the assembly and masking of datasets of proteins likely to share motifs, since the motifs are typically short (between 3 and 10 amino acids in length), so that potential signals can be easily swamped by the noise of stochastically recurring motifs. Focusing on disordered regions of proteins, where SLiMs are predominantly found, and masking out non-conserved residues can reduce the level of noise but more work is required to improve the quality of high-throughput experimental datasets (e.g. of physical protein interactions) as input for computational discovery
Exploring Emptiness: An Investigation of MA and MU in My Sonic Composition Practice
No full textThe commentary investigates Japanese aesthetics of space, silence and emptiness - ma and mu - that informed my compositional practice during the research period 2012 - 2015. The portfolio comprises text compositions and sound installations in which forms of micro events and sustained events are employed. Throughout, the emphasis is on my personal engagement with, and manifestation of emptiness that concerns a particular model of listening and perception.
Chapter 1 discusses six primary research areas: ma and mu, material, text, form, listening and perception. Firstly, I introduce ma and mu by examining noh culture and Zeami's teaching of senu hima (where there is no-action) in the context of my personal approaches to music. The following subjects are then used to contextualise my PhD practice by means of examples from various composers and visual artists. Here, these particular and enigmatic concepts are explored through Japanese art as well as Western contemporary works by Alvin Lucier, Eliane Radigue and those of the Wandelweiser collective.
Part 2 provides contextual commentaries on selected compositions from the portfolio that mostly articulate my aesthetics in relation to the topics covered in Chapter 1. koso koso addresses my methodologies to investigate the essence of senu hima, followed by treow that discusses my approach to materials and the importance of space. I move on to grade two and grade two extended in order to examine text scores, and then, look into Espèces d'espaces 03 and 04 as examples of musical forms that I employ.
Finally, listening and perception are investigated through the compositions gnome and con.de.structuring. Throughout, I describe how my works explore emptiness as a result of my particular emphasis on listening over composing
The construction of Karen Karnak: The multi-author-function
No full textThis thesis is situated within the comparatively recent developments of Web 2.0 and the emergence of interactive WikiMedia, and explores the mode of authorship within a Read/Write culture compared to that of a Read/Only tradition. The hypothesis of this study is that the role of the audience has become merged with the author, and as such, represents new functions and attributes, distinct from a more conventional concept of authorship, in which the roles of audience and author are more separate. Read/Write and participatory culture, as defined by this study, is focused on collaboration, and includes the influences of D.I.Y. culture, Open-Source practices and the production of text by multiple authors. Multi-authorship presents a re-thinking of several concepts which support the notion of the individual author, since the focus of multi-authorship is not on attribution and ownership of a finished text, but on the continued malleability of a text. Modes of multi-authorship, demonstrated in the use of the pseudonyms Alan Smithee and Karen Eliot, represent declarative authors whose names signify multiple origins, whilst concurrently indicating a distinct body of work. The function of these names form an important context to this study, since primary research involves the construction of an experimental mode of multi-authorship utilising WikiMedia technology and the interaction of thirty nine participants, who are invited to create a body of work under the collective pseudonym Karen Karnak. The data generated by this experiment is analysed using aspects of Michel Foucault's author-function to identify and determine power structures inherent in the WikiMedia context. The interplay of power structures, including concepts such as identity, ownership and the body of work, affect the resulting mode of authorship and contribute to the construction of Karen Karnak, suggesting further areas of research into the emerging multi-author
A note on Kim-Ma characterization of the Hilbert ball
No full textThis is an open access article under the CC BY license.[No abstract available]Kortney Rose Foundation, KRF, (2002-070-C00005); National Research Foundation of Korea, NRF* Corresponding author. E-mail addresses: [email protected] (K.-T. Kim), [email protected] (D. Ma). 1 Research supported in part by the grant KRF 2002-070-C00005 from The Korea Research Foundation
Localized physical vapor deposition via focused laser spike dewetting of gold thin films for nanoscale patterning
No full textFocused laser spike (FLaSk) excitation has been demonstrated as a reliable technique for the patterning of micro-to-nanoscale features locally by thermocapillary shear of thin films. Recent work on polymer thin films has revealed that overlapping laser scans can leverage coupled thermal and fluid effects to create subwavelength patterns. Compared to polymeric films, metallic thin films possess both a lower melt viscosity and higher surface tension. Here we investigate overlapping effects in the dewetting of ~15 nm gold thin films on borosilicate and quartz glass substrates with a 532 nm continuous wave laser. During this process, FLaSk initiates capillary and thermocapillary dewetting simultaneously. Further, the low oxidation potential and high vapor pressure of gold lead to non-equilibrium vaporization during heating. Since the parameters of overlapping scans control the amount of material that is heated and to what temperature it is heated, selection of laser power, scanning distance, writing speed, and numerical aperture results in particles with different sizes and spacing deposited on the writing substrates or a positioned superstrate through a laser-induced localized physical vapor deposition (LILPVD) process. If the laser parameters are selected within a specific working range, uniform or periodic particle distributions can be repeatably deposited in this fashion, which can then be used as seeds for nanomaterial growth. In addition, if the substrate melts during FLaSk, the viscous forces of the liquid-on-liquid dewetting broadens the range of patterning conditions by resisting the motion of the gold leading to more uniform particles over a large range of parameters.Peer reviewe
Ma Huan (original author), Wan Ming (ed.) Ming chaoben " Yingya shenglan " jiaozh
No full textPtak Roderich. Ma Huan (original author), Wan Ming (ed.) Ming chaoben " Yingya shenglan " jiaozh. In: Archipel, volume 71, 2006. Autour de la peinture à Java. Volume II. pp. 240-244
Geochemistry and U-Pb Geochronology of the 1450-1425 Ma Large Igneous Province of Eastern Laurentia and 2480-780 Ma Large Igneous Provinces of Western Laurentia
No full textMesoproterozoic magmatism that is exposed on the eastern and western margins of Laurentia (North America) are interpreted to be parts of large igneous provinces (LIP). The western margin between Kimberley (British Columbia) and Yellowstone National Park (Wyoming), and the eastern margin between Labrador City and coastal Labrador are herein referred to as western Laurentia (WL) and eastern Laurentia (EL), respectively. WL intraplate magmatism was previously divided into two LIPs the: 1) ca. 1460 Ma Moyie-Purcell LIP (MPL) which consists of the i) Purcell lavas in the USA, ii) Moyie sills of the Belt-Purcell basin iii) dykes of the Tobacco Root Mountains and 2) the ca. 780 Ma Gunbarrel LIP. The MPL is composed of tholeiitic basalts, and associated with the world class Sullivan Pb-Zn deposit. EL consists of basalts of the non-mineralized Michael-Shabogamo Gabbros (MSG).This research demonstrated that at least 17 geochemical groups are present in WL of which some belong to additional previously unrecognized events. Seven geochemical groups belong to the ca. 1460 Ma MPL; 1 with the ca. 780 Ma Gunbarrel LIP, 2 with a 1590-1550 Ma Mammoth-Western Channel LIP (MWCL); 2 with ages of 2480, and 1420 Ma; and 5 undated mafic pulses. The MWCL is similar to contemporaneous volcanic rocks within the South Australia craton, which was adjacent to NW Laurentia ca. 1590 Ma. This study proposes a shared 1590 Ma plume and LIP magmatism between Laurentia, and South Australia cratons.The MSG of EL are subalkaline basalts enriched in P2O5 and K2O and are shown to represent a single event with 2 pulses based on new U-Pb ages. Each pulse is defined by a distinct [P2O5*1000]/Zr (P/Zr) ratio: 1) a high P/Zr group at ca. 1425-1435 Ma; and 2) a low P/Zr group at ca. 1435-1450 Ma. Enrichment of P2O5 and K2O is due to melting of a metasomatized subcontinental lithospheric mantle with melting facilitated by a slab window
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