1,720,958 research outputs found
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe 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
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
Appropriate Similarity Measures for Author Cocitation Analysis
No full textWe 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
An Artificial Neural Network Framework to Predict Patients with High Likelihood of Chronic Kidney Disease
No full textChronic kidney disease (CKD) is an important health and healthcare system problem. The ability to predict which patients will develop CKD is a difficult task due to the complex nonlinear relationships among related factors. Using artificial neural networks (ANN), applied to a population 17 through 90 years of age, we achieved 97% accuracy in classification, based on standard laboratory test and patient data. The technique was also helpful in determining which features of the data are most predictive; 75% of the features were sufficient to reach this high level of accuracy
Dispelling the Myths Behind First-author Citation Counts
No full textWe 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
Direct Identification & Classification of Leishmania Species from Biopsy Samples by Oxford Nanopore Sequencing
No full textBackground and aim
Cutaneous Leishmaniasis (CL) is a major public health threat in Saudi Arabia with an average
of 2500 cases per year (Abuzaid et al., 2017). The disease is caused by over 20 species of the
genus Leishmania and manifests as ulcerating skin lesions that can lead to life-long scars
(Abuzaid et al., 2017; Ministry of Health, 2019). Traditional parasitological techniques (e.g.,
microscopy and immunodiagnostics) are considered the gold standard; however, they cannot
differentiate between the various Leishmania species. Although molecular techniques, such
as polymerase chain reaction along with consecutive restriction fragment length
polymorphism (PCR RFLP) or next-generation sequencing, can identify species of Leishmania
(Domagalska et al., 2019), they have limited clinical use. A rapid and accurate Leishmania
identification and classification protocol that can aid in clinical decision-making would be
expected to meet a real clinical need. In this study, we identify Leishmania species directly
from biopsy samples using Oxford nanopore sequencing technology (ONT).
Methods
DNA extracted from CL biopsy samples (data and protocol published Al-Rashed et al., 2022)
was used to prepare 3 multiplexed ONT sequencing libraries using the native barcoding kit
SQK-NBD114 and a single-sample sequencing library using SQK-LSK224. Multiplex libraries
were sequenced on MinION R10 flow cells and single samples were sequenced on Flongle R10
flow cell. All samples have been confirmed to be Leishmania positive using PCR RFLP and
Sanger sequencing to classify them into species.
Reads were base called with Guppy on high-accuracy, adapters and barcodes were trimmed
using Porechop, low-complexity and low-quality reads were filtered using Filtlong, and human
DNA was removed before further processing using Minimap2 alignment to human reference
genome GRCh38. Reads were classified into Leishmania species using Kraken2 run on a
custom-built database containing 31 Leishmania genome assemblies from RefSeq.
Results
We first sequenced three samples multiplexed on a single MinION flow cell to test if
Leishmania reads can be recovered from biopsy samples rich in human DNA. We obtained
~3Gbs of data per sample with a total throughput of ~10Gbs. Using genome alignment, we
estimate Leishmania DNA to encompass ~0.1% of the data. In order to accurately detect and
classify Leishmania species, we developed a bioinformatic pipeline (see methods) that pre-
process the data and assign reads into species using unique k-mers. Using this pipeline, we
were able to identify Leishmania in all three samples and were able to classify them up to the
species level. Second, we tested if ONT adaptive sampling technology can be used to enrich
Leishmania reads. We ran the same sequencing library from the previous experiment on a
new MinION flow cell and enabled adaptive sequencing by enriching reads aligning to the
Leishmania genome. This did not increase the ratio of Leishmania reads compared to the first
sequencing run. We then tested if adaptive sampling by depleting human reads could offer
better enrichment. We find that depleting human reads offer better enrichment (0.1% vs
3.6%) than directly enriching for Leishmania reads. Lastly, we tested if we could multiplex
more samples on a single flow cell to reduce the total cost of sequencing. We multiplexed 15
Leishmania samples and a single negative control sample on a single MinION cell and obtained
3Gbs of total throughput with human read depletion. Leishmania DNA was detected in all 15
samples; however, only 10 out of 15 (66.6%) samples were positive for Leishmania using our
bioinformatic processing. Only a single misclassified Leishmania read was detected in the
negative control sample.
Conclusion
ONT proved able to detect and classify leishmania to the species level directly from CL biopsy
samples. Deep sequencing (> 1Gb per sample) was very sensitive (100% accuracy with and
without adaptive sampling), but low depth sequencing (30Mb-150Mb per sample) had a
modest sensitivity (66.6% with adaptive sampling). This information is crucial to develop a
rapid and accurate Leishmania identification and classification protocol that can aid in clinical
decision-making
An Unexplored Genome Insulating Mechanism in Caenorhabditis Elegans
No full textCaenorhabditis Elegans genome maintains active H3K36me3 chromatin domains interspersed with repressive H3K27me3 domains on the autosomes’ distal ends. The mechanisms stabilizing these domains and the prevention of position-effect variegation remains unknown as no insulator elements have been identified in C. elegans. De-novo motif discovery applied on mes-4 binding sites links the H3K36me3-specific methyltransferase to a class of non-coding DNA known as Periodic An/Tn Clusters (PATCs). PATCs display characteristics of insulator elements such as local nucleosome depletion and their restriction to genes with specific expression profiles and chromatin marks. Finally, I describe a set of experiments to further investigate the role of PATCs and mes-4 in the maintenance of stable chromatin domains using a synthetic biology approach
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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