1,721,043 research outputs found
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
Innate immune responses induced by lipopolysaccharide and lipoteichoic acid in primary goat mammary epithelial cells
No full textAbstract Background Innate immune responses induced by in vitro stimulation of primary mammary epithelial cells (MEC) using Gram-negative lipopolysaccharide (LPS) and Gram-positive lipoteichoic acid (LTA) bacterial cell wall components are well- characterized in bovine species. The objective of the current study was to characterize the downstream regulation of the inflammatory response induced by Toll-like receptors in primary goat MEC (pgMEC). We performed quantitative real-time RT-PCR (qPCR) to measure mRNA levels of 9 genes involved in transcriptional regulation or antibacterial activity: Toll-like receptor 2 (TLR2), Toll-like receptor 4 (TLR4), prostaglandin-endoperoxide synthase 2 (PTGS2), interferon induced protein with tetratricopeptide repeats 3 (IFIT3), interferon regulatory factor 3 (IRF3), myeloid differentiation primary response 88 (MYD88), nuclear factor of kappa light polypeptide gene enhancer in B-cells 1 (NFKB1), Toll interacting protein (TOLLIP), and lactoferrin (LTF). Furthermore, we analyzed 7 cytokines involved in Toll-like receptor signaling pathways: C-C motif chemokine ligand 2 (CCL2), C-C motif chemokine ligand 5 (CCL5), C-X-C motif chemokine ligand 6 (CXCL6), interleukin 8 (CXCL8), interleukin 1 beta (IL1B), interleukin 6 (IL6), and tumor necrosis factor alpha (TNF). Results Stimulation of pgMEC with LPS for 3 h led to an increase in expression of CCL2, CXCL6, IL6, CXCL8, PTGS2, IFIT3, MYD88, NFKB1, and TLR4 (P < 0.05). Except for IL6, and PTGS2, the same genes had greater expression than controls at 6 h post-LPS (P < 0.05). Expression of CCL5, PTGS2, IFIT3, NFKB1, TLR4, and TOLLIP was greater than controls after 3 h of incubation with LTA (P < 0.05). Compared to controls, stimulation with LTA for 6 h led to greater expression of PTGS2, IFIT3, NFKB1, and TOLLIP (P < 0.05) whereas the expression of CXCL6, CXCL8, and TLR4 was lower (P < 0.05). At 3 h incubation with both toxins compared to controls a greater expression (P < 0.05) of CCL2, CCL5, CXCL6, CXCL8, IL6, PTGS2, IFIT3, IRF3, MYD88, and NFKB1 was detected. After 6 h of incubation with both toxins, the expression of CCL2, CXCL6, IFIT3, MYD88, NFKB1, and TLR4 was higher than the controls (P < 0.05). Conclusions Data indicate that in the goat MEC, LTA induces a weaker inflammatory response than LPS. This may be related to the observation that gram-positive bacteria cause chronic mastitis more often than gram-negative infections
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
Bioinformatics analyses of non-coding genomic elements
Full text link"Mammalian genomes consist primarily of non-coding sequences (Kellis et al. 2014). Originally castigated as ""junk DNA"", many non-coding regions have now been characterized as having functional roles, or have been determined to be the causal agent for diseases. Additionally, sequences that are non-functional can be used as neutral markers for population genetics. Determining the role of non-coding sequences or finding sequences usable as neutral markers is computationally and biologically non-trivial. However, recent advances in molecular biology, in particular the reduced cost of next-generation sequencing (NGS), have enabled new experiments that involve these sequences. I will discuss studies using bioinformatics that leveraged these advances to characterize three types of non-coding sequences: endogenous retroviruses, microsatellite markers and transcription factor binding sites. I conducted the bioinformatics design, coding and analyses, working with collaborators who verified findings in the laboratory.
The only retrovirus known to be currently transitioning from exogenous to endogenous form is the koala retrovirus (KoRV), making koalas (Phascolarctos cinereus) ideal for examining the early stages of retroviral endogenization. In the first study, I developed a bioinformatics routine to identify distinct retroviral integrants from NGS reads of KoRV retrovirus flanks isolated using koala genomic DNA. In the second study, I developed computationally efficient, user-friendly software that would identify polymorphic microsatellite loci using NGS reads, then design oligonucleotide primers appropriate for amplifying those loci. We developed this software to enable studies to improve understanding of population structure, estimate population size and estimate genetic diversity in genetically depauperate wildlife species. In the third study, I developed a bioinformatics pipeline to characterize gene expression changes during development in the fetal limb tissue of several mammalian species, to better understand the mechanistic differences across evolutionary lineages. We compared development in four species of mammals. The house mouse was used since it is a well-characterized model organism with five digits. The domestic pig was used since it is a well-studied agricultural animal and a model for digit reduction. A species of bat was used since bats undergo wing development. Finally, a species of opossum was used as an outgroup to the three eutherian species."Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2018-05-01The student, Kai Zhao, accepted the attached license on 2016-04-13 at 16:26.The student, Kai Zhao, submitted this Dissertation for approval on 2016-04-13 at 16:37.This Dissertation was approved for publication on 2016-04-15 at 08:13.DSpace SAF Submission Ingestion Package generated from Vireo submission #9211 on 2016-07-07 at 14:16:40Made available in DSpace on 2016-07-07T21:14:41Z (GMT). No. of bitstreams: 3
ZHAO-DISSERTATION-2016.pdf: 2247656 bytes, checksum: 30daef0d3c41884b383500f38d651072 (MD5)
LICENSE.txt: 4205 bytes, checksum: c2cd4b73b8d68ead2a5bcb54af6c557c (MD5)
PROQUEST_LICENSE.txt: 4551 bytes, checksum: ca00a57bf5891e20f293755778579a91 (MD5)
Previous issue date: 2016-04-15Embargo set by: Seth Robbins for item 93249
Lift date: 2018-07-07T21:14:52Z
Reason: Author requested closed access (OA after 2yrs) in Vireo ETD systemEmbargo set by: Seth Robbins for item 93249
Lift date: 2018-07-07T21:18:16Z
Reason: Author requested closed access (OA after 2yrs) in Vireo ETD systemLimited Restriction Lifted for Item 93249 on 2018-07-08T09:15:23Z
Porcine model of xenobiotic metabolism
Full text linkA xenobiotic is a foreign chemical substance found in the environment. The body removes xenobiotics by xenobiotic metabolism. Drug metabolizing enzymes (DMEs) play central roles in the metabolism, elimination, and detoxification of xenobiotics introduced into the body. Orphan nuclear receptors play crucial role in regulation of the expression of DMEs. The pig has quickly grown into an important biomedical research tool over the past few decades. The pig is an appropriate animal model for the investigation of xenobiotic disposition, as the transporters and CYP enzymes are very similar to those in humans. The characterization of porcine drug metabolism genes and the genes involved in regulating drug metabolism can provide insights into human drug metabolic diseases and individual variability of responses toward a drug. The tissue- and stage-specific expression of the nuclear receptors in pigs and their comparison to humans will be of great interest. Consequently, the goal of the proposal is to validate pig as a model of xenobiotic metabolism in order to get a better understanding of the pharmacokinetic properties of the xenobiotics. Expression of orphan nuclear receptors were screened across various porcine organs (liver, kidney, lung, small intestine, spleen, pancreas, heart, brain and skeletal muscle). Analysis of the mRNA expression levels of porcine orphan nuclear receptors in total RNA from various porcine organs was also performed by real time reverse transcriptase PCR. Expression of all the porcine nuclear receptors studied except (PPARγ) was detected in the liver and kidney. Most of the nuclear receptors showed higher expression in the liver. The tissue distribution and the expression profiles of the porcine nuclear receptors were consistent with those of human. To evaluate the effect of xenobiotic exposure on the expression pattern of the nuclear receptors, expression pattern of nuclear receptors were evaluated in three different developmental stages i.e; three month old fetus, one month old piglet and one year old adult pig. The expression levels of the nuclear receptors in adult tissues were higher than that of one month old piglets which in turn were higher than those of a three month old fetal piglet. Porcine orphan nuclear receptors liver X receptor alpha (LXRα), liver X receptor beta (LXRβ) and constitutive androstane receptor (CAR) were cloned and the sequence analysis revealed eight novel transcript variants for LXRα and LXRβ each and five novel transcript variants for CAR. The expression profiles and the physiochemical properties of the novel identified transcript variants were analyzed. Further, we developed and characterized a porcine hepatocyte cell line representative of human primary hepatocytes to support drug toxicity and metabolism assessments. Three independent hepatocyte cell lines were developed from three different Oncopigs and all of them expressed hepatocyte specific and most important drug metabolism and regulation genes comparable to those porcine primary hepatocytes. We evaluated the effect of selective CYP modulators on three porcine hepatocyte cell lines. All the three independent porcine hepatocyte cell lines behaved the same way and the gene regulation pattern in hepatocyte cell lines was similar to that of primary hepatocytes and human models. These findings indicate that this porcine hepatocyte cell line represents a useful and predictive model for high throughput screening of new drugs as well as studies on metabolism and hepatotoxicity of chemicals.Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2018-08-01The student, Arun De, accepted the attached license on 2016-07-12 at 13:18.The student, Arun De, submitted this Dissertation for approval on 2016-07-12 at 13:23.This Dissertation was approved for publication on 2016-07-12 at 15:10.DSpace SAF Submission Ingestion Package generated from Vireo submission #9889 on 2016-11-10 at 12:25:16Made available in DSpace on 2016-11-10T18:42:57Z (GMT). No. of bitstreams: 3
DE-DISSERTATION-2016.pdf: 5865976 bytes, checksum: 9e411af9db1812c0a570b3001552fcb6 (MD5)
LICENSE.txt: 4204 bytes, checksum: d326edd22580bf23e7cc9ee7f3ffe4ec (MD5)
PROQUEST_LICENSE.txt: 4550 bytes, checksum: 64feb89b1969f1ce713018d0addee0a9 (MD5)
Previous issue date: 2016-07-12Embargo set by: Seth Robbins for item 95479
Lift date: 2018-11-10T18:43:22Z
Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD systemU of I Only Restriction Lifted for Item 95479 on 2018-11-11T10:15:24Z
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
Local and regional scale genetic variation in the Cape dune mole-rat, Bathyergus suillus
Full text linkThe distribution of genetic variation is determined through the interaction of life history, morphology and habitat specificity
of a species in conjunction with landscape structure. While numerous studies have investigated this interplay of factors in
species inhabiting aquatic, riverine, terrestrial, arboreal and saxicolous systems, the fossorial system has remained largely
unexplored. In this study we attempt to elucidate the impacts of a subterranean lifestyle coupled with a heterogeneous
landscape on genetic partitioning by using a subterranean mammal species, the Cape dune mole-rat (Bathyergus suillus), as
our model. Bathyergus suillus is one of a few mammal species endemic to the Cape Floristic Region (CFR) of the Western
Cape of South Africa. Its distribution is fragmented by rivers and mountains; both geographic phenomena that may act as
geographical barriers to gene-flow. Using two mitochondrial fragments (cytochrome b and control region) as well as nine
microsatellite loci, we determined the phylogeographic structure and gene-flow patterns at two different spatial scales
(local and regional). Furthermore, we investigated genetic differentiation between populations and applied Bayesian
clustering and assignment approaches to our data. Nearly every population formed a genetically unique entity with
significant genetic structure evident across geographic barriers such as rivers (Berg, Verlorenvlei, Breede and Gourits Rivers),
mountains (Piketberg and Hottentots Holland Mountains) and with geographic distance at both spatial scales. Surprisingly,
B. suillus was found to be paraphyletic with respect to its sister species, B. janetta–a result largely overlooked by previous
studies on these taxa. A systematic revision of the genus Bathyergus is therefore necessary. This study provides a valuable
insight into how the biology, life-history and habitat specificity of animals inhabiting a fossorial system may act in concert
with the structure of the surrounding landscape to influence genetic distinctiveness and ultimately speciation.A Centre for Invasion Biology stipend to BJVV.http://www.plosone.orgam201
- …
