1,720,975 research outputs found
Statistically learning Archean carbonate diagenesis
No full textGeochemical data are often very noisy due to the large natural heterogeneity of the geological materials as well as oversimplification of rock classification. This has serious repercussions on the precision of our knowledge of the deep past as we often rely solely on geochemical proxies to investigate the geological evolution of Archean and Proterozoic environments. Here statistical learning procedures were applied to achieve unbiased classification of Neoarchean stromatolitic dolostone textures on the basis of the distribution of their trace elements and rare earth elements (REE) investigated through laser ablation induced coupled plasma - mass spectrometry (LA-ICP-MS). Multivariate statistical analyses and supervised statistical learning have revealed that different dolomite fabrics, thought as products of aggrading diagenesis and recrystallization, are in fact chemically indistinguishable. The diagenetic processes that cause the re-crystallization of dolomite and the consequent change of textures, is not affecting the distribution of major and trace elements inherited by the depositional environment or during early stages of diagenesis. At the same time the algorithm has revealed that an optically homogeneous microcrystalline dolomite sample may in fact be geochemically inhomogeneous because of processes of ripening and recrystallization occurred at an early stage of marine diagenesis and that have contributed to element mobilization. Statistical learning has succeeded in recognizing chemofacies which not always overlap with dolomite textures and fabrics highlighting the importance of crystallographic and diagenetic studies before any study of carbonates as geochemical proxies
Statistical methods for identification of NF-κB related genes and their expression profiles in channel catfish after bacterial infection
Full text linkInteractions of NF-κB family, IκB family and IKK complex are key components of NF-κB pathway that is essential for many biological processes including innate and adaptive immunity, and inflammation and stress responses. Despite their importance, systematic analysis of these genes in fish has been lacking. In this project, statistical analysis of NF-κB related genes and their gene expression after bacterial infection was conducted with channel catfish.
A total of thirteen NF-κB related genes were identified in the channel catfish genome, including five NF-κB family genes, five IκB family genes and three IKK complex genes. To confirm the annotation of these thirteen NF-κB related genes, maximum likelihood methods were applied to construct phylogenetic tree of each gene with various species. The reliability of these constructed phylogenetic trees was confirmed by the bootstrap test. Syntenic analysis was used to further determine the annotation of those genes which failed to be confirmed by phylogenetic analysis. To determine the evolutionary patterns of these NF-κB related genes, likelihood ratio test was applied for detecting their selective pressures during evolution. The result indicates that negative selection may play a crucial role in the adaptive evolution of these NF-κB related genes.
Expression profiles of NF-κB related genes after Flavobacterium columnare (columnaris) infection were determined by conducting both real-time PCR analysis of different tissues and Kal’s Z test with the existing RNA-Seq dataset. The majority of NF-κB related genes were significantly regulated in mucosal tissues of gill, skin and intestine after columnaris infection, indicating their potential involvement in host defense responses to bacterial infection. Distinct expression patterns of NF-κB related genes were observed in the susceptible and resistant catfish in response to columnaris infection, suggesting that expression of these genes may contribute to the variations in disease resistance/susceptibility of catfish
Nonparametric Analysis of Temperature and Carbon Source Effects on vfr Gene Expression and Regulation
Full text linkSince temperatures and carbon sources are potential conditions that affect gene expression and regulation, experiments of vfr expression and regulation in the organism Pseudomonas aeruginosa were designed and performed to address the following questions of interest: i) Do low or high temperature (30℃/42℃) have an effect on vfr expression? ii) Do low or high temperature (30℃/42℃) have an effect on vfr regulations controlled by tmRNA, GacA or GacS, which were three potential vfr regulators found in the previous laboratory work? iii) Do carbon sources like Glycerol, Glucose or Succinate have an effect on vfr expression? And iv) Do these carbon sources have an effect on tmRNA, GacA or GacS controlled vfr regulation individually?
As our data (both temperatures and carbon sources) did not satisfy the normality assumption, a set of distribution-free nonparametric analyses were applied in this work. For studying the effects of the temperatures and carbon sources on vfr expressions, regulations as well as their variances, powerful and robust nonparametric analysis for location, Nemenyi test, and the Anasari-Bradley test for scale comparison were used to make final conclusions.
According to the Nemenyi test, temperatures (30℃ or 42℃) affected vfr expression and but not the tmRNA, GacA or GacS controlled vfr regulations in P.aeruginosa. In addition, Ansari-Bradley test indicated that, the low temperature would not affect the variances until the late-log phase, while the high temperature affected the variances of vfr expression in P. aeruginosa from mid-log to late-log phase, but not to the end. Furthermore, high temperature affected all of the variances of tmRNA, GacA and GacS controlled vfr expression in mid-log, but only GacS regulated vfr expression in late-log, and only tmRNA dependent expression at the stationary phase in P. aeruginosa., while low temperature affected the variances of GacA regulated vfr expression at the mid-log phase, and affected the variances of tmRNA and GacS regulated expression at the late-log phase in P. aeruginosa, and at the stationary phase, none of the variances of these vfr regulations were altered by the low temperature.
In order to test the effects of carbon sources on vfr expressions and regulations, similar analyses were applied to the carbon source study. According to Nemenyi approach, vfr expressions in P. aetuginosa were not be affected by any supply of Glycerol, Glucose or Succinate in NCE medias when they served as sole carbon sources. Also, since all of the tmRNA, GacA and GacS controlled vfr regulations functioned very well, vfr regulations in P. aetuginosa were also not affected in Glycerol, Glucose or Succinate supplemented NCE medias. Therefore, we conclude that carbon sources would affect neither vfr expressions nor the tmRNA, GacA and GacS controlled regulations in P. aetuginosa. According to the Ansari-Bradley test, the variances of vfr expressions in P. aetuginosa were not affected by the supply of Glycerol, Glucose or Succinate in NCE medias when they were served as sole carbon sources. The variances of tmRN, GacA, GacS controlled vfr regulations were not altered too. In conclusion, supply of Glycerol, Glucose or Succinate in NCE medias as the sole carbon sources would not affect the variances of vfr expressions in P. aetuginosa. Carbon sources also did not affect tmRNA, GacA and GacS controlled vfr regulations
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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