131,292 research outputs found
Effects of Sidewall Compression and Relaminarization in a Scramjet Inlet
No full textThis paper presents the numerical simulations and the performance analysis of a scramjet inlet as part of a combined experimental and numerical study. A well-validated finite volume flow solver was used to simulate a scramjet inlet with a double ramp configuration for outer compression, including varying degrees of sidewall compression. The computed wall pressure and heat transfer in the symmetry plane are in close agreement with the measurements, and the numerical results indicate that the weak sidewall compression alters the inlet performance significantly. The effects of partial relaminarization over the expansion corner, before the interior part of the inlet, is isolated and investigated in both the experiment and simulation. It is shown that relaminarization of a boundary layer is predicted accurately using the current numerical methods. This work represents a contribution to the understanding of the effects of sidewall compression and relaminarization in designing a scramjet inlet
Acid monolayer functionalized iron oxide nanoparticles as catalysts for carbohydrate hydrolysis
No full textSuperparamagnetic iron oxide nanoparticles were functionalized with a quasi-monolayer of 11-sulfoundecanoic acid and 10-phosphono-1-decanesulfonic acid ligands to create separable solid acid catalysts. The ligands are bound through carboxylate or phosphonate bonds to the magnetite core. The ligand-core bonding surface is separated by a hydrocarbon linker from an outer surface with exposed sulfonic
acid groups. The more tightly packed monolayer of the phosphonate ligand corresponded to a higher sulfonic acid loading by weight, a reduced agglomeration of particles, a greater tendency to remain suspended in solution in the presence of an external magnetic field, and a higher catalytic activity per sulfonic acid group. The particles were characterized by thermogravimetric analysis (TGA), transmission
electron microscopy (TEM), potentiometric titration, diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), inductively coupled plasma optical emission spectrometry (ICP-OES), and dynamic light scattering (DLS). In sucrose catalysis reactions, the phosphonic–sulfonic nanoparticles (PSNPs) were seen to be incompletely recovered by an external magnetic field, while the carboxylic–sulfonic nanoparticles (CSNPs) showed a trend of increasing activity over the first four recycle runs. The activity of the acid-functionalized nanoparticles was compared to the traditional solid acid catalyst Amberlyst-15 for the hydrolysis of starch in aqueous solution. Catalytic activity for starch hydrolysis was in the order PSNPs > CSNPs > Amberlyst-15. Monolayer acid functionalization of iron oxides presents a novel strategy for the development of recyclable solid acid catalysts
MeSH term explosion and author rank improve expert recommendations
No full textInformation overload is an often-cited phenomenon that reduces the productivity, efficiency and efficacy of scientists. One challenge for scientists is to find appropriate collaborators in their research. The literature describes various solutions to the problem of expertise location, but most current approaches do not appear to be very suitable for expert recommendations in biomedical research. In this study, we present the development and initial evaluation of a vector space model-based algorithm to calculate researcher similarity using four inputs: 1) MeSH terms of publications; 2) MeSH terms and author rank; 3) exploded MeSH terms; and 4) exploded MeSH terms and author rank. We developed and evaluated the algorithm using a data set of 17,525 authors and their 22,542 papers. On average, our algorithms correctly predicted 2.5 of the top 5/10 coauthors of individual scientists. Exploded MeSH and author rank outperformed all other algorithms in accuracy, followed closely by MeSH and author rank. Our results show that the accuracy of MeSH term-based matching can be enhanced with other metadata such as author rank
Epigenetic regulation of endogenous plant pararetroviruses
No full textThis thesis focuses on epigenetic processes involved in the regulation of gene expression in endogenous pararetroviruses (EPRVs), exemplified by endogenous Petunia vein clearing virus (ePVCV-1) and its episomal form, PVCV. Since ePVCV-1/PVCV was found to have features characteristic of retrotransposon and endogenous retroviruses (Richert-Poggeler and Shepherd, 1997), detailed analysis of these retroelements in different systems gives a deep insight to understand the interconnection of these elements and their regulation by the host cellular machinery as described in chapter one.
Chapter two describes the different silencing states of ePVCV-1 in two distinct Petunia hybrida lines, “white 138” (W138) and “rose du ciel” (Rdc). Despite of ePVCV-1 integration into the pericentromeric regions of the Petunia hybrida chromatin, we found that this position still allows for a low level of transcription that increases with increasing plant age and is higher in W138 than Rdc. To correlate these findings with epigenetic marks, we compared these cultivars in respect to DNA- and histone-methylation and siRNA production. Using bisulfite treatment, ePVCV-1 sequences were found to be methylated at cytosines in all contexts. Astonishingly, however, in both hosts the methylation rate in the non-coding region containing the promoter is relatively low. This might indicate a special ability of the viral promoter to escape complete inactivation by methylation. In Rdc, nearly all histones covering the ePVCV-1 coding region were methylated at lysine 9 of histone 3 (H3K9), a flag for heterochromatin, while in W138 about half of them were of the H3K9- and half of the H3K4-type, the latter representing active chromatin. Interestingly and in accordance with the DNA methylation data, the H3K4/H3K9 ratio was relatively high for the promoter region of both cultivars. The higher H3K4/H3K9 ratio in W138 correlates with an increased rate of ePVCV-1 induction. Furthermore, we show the production of siRNAs of three different size classes (24, 22 and 21 nt) in both cultivars, all of
which are weaker in W138 than in Rdc. Together our observations indicate that W138 is less efficient in silencing of the endogenous viral sequences than Rdc.
In chapter three, I investigated the promoter region of PVCV and determined its ability to direct transcription in transgenic plants. Furthermore, I analyzed the regulatory elements of this particular promoter in comparison with those of other plant pararetrovirus promoters. In particular I studied the functionality of an as-1 like element and its contribution to PVCV promoter expression. Although originally of medium strength, the promoter could be improved to about 50% strength of that of the CaMV 35S promoter by “repairing“ a pair of degenerated as-1 enhancer elements. We show, that the promoter includes upstream and downstream enhancer elements, and that it can be improved considerably by restoring two degenerated as-1 elements.
The concept of creating virus-resistant plants by transformation with genes derived from the pathogen genome is a well-exploited and highly effective procedure to fight viruses as causal agents of diseases in plants (Fichen and Beachy, 1993). Recently it has been demonstrated that RNA interference (RNAi) can be successfully triggered against plant viruses by transient expression of an inverted repeat of target sequences (Pooggin et al., 2003; Tenllado et al., 2004). In chapter four, we use this technique to develop RNA-mediated banana streak virus resistance via TGS and/or PTGS and the method should prevent the outbreak of virus infection upon rare spontaneous induction of endogenous BSV in tissue culture.
Chapter five is a publication in EMBO journal to which I contributed in major ways. This paper describes the production of cloned PVCV originating directly from Petunia plants and from a Petunia gene library. Our findings allowed comparative and direct analysis of horizontally and vertically transmitted virus forms and demonstrated their infectivity using biolistic transformation of a provirus-free petunia species. Some integrants within the genome of P.hybrida were found to be arranged in tandem, allowing direct release of virus by transcription. In addition to known inducers of endogenous pararetroviruses, such as genome hybridization, tissue culture and abiotic stresses, we observed
activation of PVCV after wounding. Our data also support the hypothesis that the host plant uses DNA methylation to control the endogenous pararetrovirus.
In a preamble I point out, which part of this paper is based on my own experimentation and interpretation. on to control the endogenous pararetrovirus.
In a preamble I point out, which part of this paper is based on my own experimentation and interpretation
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
"Closing the R&D Gap, Evaluating the Sources of R&D Spending"
No full textBoth spending and tax policies have been implemented in the United States with the goal of stimulating private sector research and development (R&D). Karier questions whether current R&D policy, especially the research and experimentation tax credit, can contribute to closing the gap between nondefense expenditures on R&D in the United States and such expenditures in other countries, such as Japan and Germany. He also explores possible changes to our current R&D policy to make it more effective.
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
Scholarly Communication and Publishing Lunch and Learn Talk #11: The ULS Open Access Author Fee Fund
No full textAt the May 2014 talk, you will learn about the ULS Open Access Author Fee Fund--what it is, why we do it, how it works, and how the program is going so far
Isolation and characterization of "Arabidopsis" mutants with altered homologous recombination levels : a new function for an INO80 SWI/SNF ATPase
No full textHomologous recombination (HR) in eukaryotic organisms serves a dual role in providing
genetic flexibility by creating novel sequence assortments upon meiosis and in maintaining
genome integrity through DNA repair in somatic tissues. HR represents an alternative
pathway to non-homologous end-joining (NHEJ) for the repair of double-strand breaks
(DSB). The repair by NHEJ may not preserve the integrity of the genetic information
whereas the HR pathway is more faithful. The choice of a pathway to repair DSBs is thus
crucial for genome integrity and evolution, especially in plants where the germline is only
determined late during development. Very little is known on what influences the choice of
the pathway taken, but chromatin structure at the site of a lesion likely will play a major
role in the recruitment of repair enzymes and thereby the choice of repair pathway. As a
consequence, various proteins that are not part of the core of the recombination machinery
may directly participate in the regulation of HR. At the time this work was initiated, no
plant gene involved in the HR pathway or its regulation was characterized yet. As plants
are powerful genetic tools especially for screening, we decided on designing and
conducting a genetic screen to identify plant genes involved in HR.
Here I describe a genetic screen in Arabidopsis thaliana for mutants with altered
somatic recombination levels and the characterization of the resulting mutant candidates.
For the screen, I used a stably integrated luciferase based intrachromosomal HR substrate
and a T-DNA construct designed for activation tagging as a mutagenic agent. Out of 19520
individual transformants tested, 37 exhibited an altered HR phenotype. Nine of them were
sterile and/or exhibited important developmental or growth phenotypes that precluded the
formation of progeny seeds, which is more than the average number of sterile plants
expected. However, in most cases the altered recombination phenotype was lost in the
offspring. To characterize the mutations, I cloned all the T-DNA insertion sites by plasmid
rescue and determined the potential target genes. I discuss the genes likely to be responsible
of the observed phenotype.
Here I report the thorough analysis of a mutant in the Arabidopsis INO80 ortholog of
the SWI/SNF ATPase family, which shows a reduced frequency of HR. In contrast,
sensitivity to genotoxic agents and efficiency of T-DNA integration remain unaffected.
This suggests that INO80 is a positive regulator of HR, while not affecting other repair
pathways. Further, transcriptionaly silent TSI loci are not reactivated in absence of INO80,
suggesting that Arabidopsis INO80 function is independent of transcriptional silencing.
Using whole genome expression studies by microarray profiling I show evidence that
INO80 regulates a small subset of Arabidopsis genes, suggesting a dual role for INO80 in
transcription and repair by HR. Moreover, the recombination-promoting function of INO80
is not likely to involve general transcriptional regulation, and the transcriptional regulation
of repair related genes is unaffected in the mutant. This is the first report of INO80 function
in a higher eukaryote. Mononucleosome binding studies support the suggestion that INO80
positively regulates HR through modification of chromatin structure at sites of DNA repair
by HR. Finally, I provide evidence for the existence and/or connectivity of INO80 with
other INO80 complex partners in Arabidopsis
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