1,720,958 research outputs found
TESE: generating specific protein structure test set ensembles
No full textTESE is a web server for the generation of test sets of protein sequences and structures fulfilling a number of different criteria. At least three different use cases can be envisaged: (i) benchmarking of novel methods; (ii) test sets tailored for special needs and (iii) extending available datasets. The CATH structure classification is used to control structural/sequence redundancy and a variety of structural quality parameters can be used to interactively select protein subsets with specific characteristics, e.g. all X-ray structures of alpha-helical repeat proteins with more than 120 residues and resolution <2.0 A. The output includes FASTA-formatted sequences, PDB files and a clickable HTML index file containing images of the selected proteins. Multiple subsets for cross-validation are also supported. AVAILABILITY: The TESE server is available for non-commercial use at URL: http://protein.bio.unipd.it/tese/
Valutazione dei principali indicatori bibliometrici relativi alle riviste scientifiche internazionali peer-reviewed ad orientamento trapiantologico.
No full textIntroduzione – L’adozione di specifici indicatori bibliometrici (IB) rappresenta una modalità di valutazione quantitativa in grado di offrire elementi utili alla valutazione della rilevanza e penetranza delle informazioni veicolate attraverso il circuito delle riviste scientifiche internazionali peer-reviewed ad orientamento trapiantologico. Metodi – Nell’ambito della base dati ISI (Institute for Scientific Information) è stata effettuata una ricerca per "subject category" finalizzata alla restituzione delle riviste di interesse trapiantologico indicizzate per il periodo 2000-2004 (n=19) [1]. Per ciascuna rivista sono stati considerati i seguenti IB/anno: numeri pubblicati, Total Cites (TC), Impact Factor (IF; n citazioni per l’anno di riferimento dei lavori pubblicati nel biennio precedente/n articoli pubblicati nel biennio precedente); Immediacy Index (IMI); Overall Articles (OA); Cited Half-life (CedHL); Citing Half-life (CngHL); non-Review Articles (non-Rev); Reviews (Rev); non-Rev/Rev ratio. Gli IB sono stati analizzati mediante statistiche descrittive, confronto tra due o più gruppi (test di Mann-Whitney od ANOVA) e correlazione non parametrica di Spearman. Risultati – Le statistiche descrittive inerenti gli IB hanno presentato i seguenti valori medi/anno: numeri pubblicati: 10.04+/-5.8 (mediana [md]: 8; range: 4 – 24); TC: 4195.66+/-6181.48 (md: 1482; range: 23 – 25722); IF: 2.11+/-1.16 (md: 2.06; range: 0.25 – 5.68); IMI: 0.34+/-0.29 (md: 0.308; range: 0.017 – 1.49); OA: 248.68+/-318.81 (md: 107; range: 26 – 1605); CedHL: 5.076+/-1.62 (md: 5; range: 1.2 – 9.7); CngHL: 6.05+/-0.62 (md: 6; range: 4 – 7.5); non-Rev: 241.2+/-319 (md: 99; range: 25 – 1605); Rev: 7.48+/-7.37 (md: 5.5; range: 0 – 32); non-Rev/Rev ratio: 43.93+/-76.08 (md: 19.6; range: 1.37 – 507). Il confronto tra gli IB stratificati per anno non ha registrato alcuna significatività statistica nel confronto tra due o più gruppi. L’IF medio calcolato per l’anno 2000 (2.00+/-0.97) è risultato privo di significatività statistica nei confronti del medesimo parametro riferito all’anno 2004 (2.26+/-1.28; P = 0.536). Una correlazione diretta significativa è stata individuata tra IF ed i seguenti IB: numeri pubblicati (r = 0.277; P = 0.013); TC (r = 0.29; P = 0.009); IMI (r = 0.763; P <0.0001); Rev (r = 0.33; P = 0.002). Una correlazione inversa significativa è stata riscontrata tra IF e CedHL (r = -0.748; P<0.0001), CngHL (r = 0.48; P<0.0001) e non-Rev/Rev ratio (r = -0.24; P = 0.031). Il coefficiente di variazione (CV) generale riferito all’IF è risultato del 54.52%; il CV dell’IF per singolo anno ha presentato per l’anno 2000 un valore del 48.73%, mentre per l’anno 2004 è risultato del 56.69%. Il CV dell’IF per singola rivista è risultato compreso tra il 6.95% ed il 30.59%. Conclusioni – L’IF delle riviste scientifiche internazionali ad orientamento trapiantologico è risultato direttamente correlato con il numero di Review pubblicate ed inversamente correlato con il non-Rev/Rev ratio. L’elevato CV generale e per rivista dell’IF può ostacolare a livello di singolo autore/gruppo di ricerca il processo decisionale circa la selezione della rivista a cui sottoporre un contributo scientifico. Bibliografia - [1]. http://jcr17.isiknowledge.com/JCR/JCR
REPETITA: detection and discrimination of the periodicity of protein solenoid repeats by discrete Fourier transform
No full textMotivation: Proteins with solenoid repeats evolve more quickly than non-repetitive ones and their periodicity may be rapidly hidden at sequence level, while still evident in structure. In order to identify these repeats, we propose here a novel method based on a metric characterizing amino-acid properties (polarity, secondary structure, molecular volume, codon diversity, electric charge) using five previously derived numerical functions.
Results: The five spectra of the candidate sequences coding for structural repeats, obtained by Discrete Fourier Transform (DFT), show common features allowing determination of repeat periodicity with excellent results. Moreover it is possible to introduce a phase space parameterized by two quantities related to the Fourier spectra which allow for a clear distinction between a non-homologous set of globular proteins and proteins with solenoid repeats. The DFT method is shown to be competitive with other state of the art methods in the detection of solenoid structures, while improving its performance especially in the identification of periodicities, since it is able to recognize the actual repeat length in most cases. Moreover it highlights the relevance of local structural propensities in determining solenoid repeats
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
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
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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