1,512 research outputs found
Analysis of the transcriptional control region of JC polyomavirus in cerebrospinal fluid from HIV-negative patients with progressive multifocal leucoencephalopathy.
No full textThe human polyomavirus JC (JCV) is the causative agent of progressive multifocal leukoencephalopathy (PML), a fatal demyelinating disease of the central nervous system (CNS). JCV has a hyper-variable non-coding transcriptional control region (TCR), which contains the origin of replication and the promoters of viral transcription and replication. The archetype form of TCR-JCV is frequently found in the urine and kidneys of healthy and immunocompromised subjects. However, the rearranged forms, possibly generated by deletion and duplication of segments of the archetype sequence, are found in the peripheral blood, cerebrospinal fluid (CSF), and brain of PML patients. Most experience on this setting has come from the human immunodeficiency virus (HIV) pandemic. Little has been described on the JCV-TCR sequences from PML-HIV-negative patients affected by other immunosuppressive disorders. The aim of this study was to analyze the JCV-TCR detected in CSF samples from 12 HIV-negative immunosuppressed patients suffering from PML and to investigate the possible role of genomic organization in the different incidences of PML in HIV-positive and HIV-negative patients. The results confirm that the JCV-TCR rearrangements play a crucial role in the development of PML, although they do not account for the higher frequency of the disease in HIV infection. These data support the hypothesis that, independently of the rearrangement patterns of JCV-TCR, the direct action of HIV together with other as yet unidentified cellular determinants can be a key to explaining the high rate of PML in HIV infection with respect to other underlying immunosuppressive conditions
Considerazioni patogenetiche sulla Leucoencefalopatia Multifocale Progressiva (PML)
No full textComunicazione oral
Prolog+CG: A Maintainer's Perspective
No full text Prolog+CG is an implementation of Prolog with Conceptual Graphs as first-class datastructures, on a par with terms. As such, it lends itself well to applications in which reasoning with Conceptual Graphs and/or ontologies plays a role. It as originally developed by Prof. Dr. Adil Kabbaj, who in 2004 turned over maintainership of Prolog+ CG to the present author. In this paper, Prolog+CG is described in terms of its history, evolution, and maintenance. A special web-enabled version of Prolog+CG is also described. Possible interoperability with CGIF and the CharGer tool are explored. Finally, we offer some general observations about the tenets that make Prolog+CG a success.</p
Voluntary corporate governance disclosure by post-apartheid South African corporations
No full textPurpose – The purpose of this paper is to investigate as to whether post-Apartheid South African (SA) listed corporations voluntarily comply with and disclose recommended good corporate governance (CG) practices and, if so, the major factors that influence such voluntary CG disclosure behaviour. Design/methodology/approach – The paper constructs a broad voluntary CG disclosure index containing 50 CG provisions from the 2002 King Report using a sample of 169 SA listed corporations from 2002 to 2006. The authors also conduct regression analysis to identify the main drivers of voluntary CG disclosure. Findings – The results suggest that while compliance with, and disclosure of, good CG practices varies substantially among the sampled companies, CG standards have generally improved over the five-year period examined. The authors also find that block ownership is negatively associated with voluntary CG disclosure, while board size, audit firm size, cross-listing, the presence of a CG committee, government ownership and institutional ownership are positively related to voluntary CG disclosure. Practical implications – These findings have important implications for policy-makers and regulators. Evidence of improving CG standards implies that efforts by various stakeholders at improving CG standards in SA companies have had some positive impact on CG practices of SA firms. However, the substantial variation in the levels of compliance implies that enforcement may need to be strengthened further. Originality/value – There is a dearth of evidence on the level of compliance with the King Report. This study fills this gap by providing evidence for the first time on the level of compliance achieved, as well as contributing generally to the literature on compliance with codes of good governance and voluntary disclosure.<br/
Identical rearranged forms of JC polyomavirus transcriptional control region in plasma and cerebrospinal fluid of acquired immunodeficiency syndrome patients with progressive multifocal leukoencephalopathy
No full textProgressive multifocal leukoencephalopathy (PML) is a fatal demyelinating disease of the central nervous system (CNS) caused by the human polyomavirus JC (JCV). JCV has a hypervariable noncoding transcriptional control region (TCR) that spans the origin of replication of the JCV genome through to the first ATG start codon for late gene transcription. The archetype form of TCR is frequently found in the urine and kidneys of healthy and immunocompromised subjects. However the rearranged forms, whose prototype is Mad-1, possibly generated by deletion and duplication of segments of the archetype sequence, are found in the brain and cerebrospinal fluid (CSF) of PML patients. In this study the authors compared JCV TCR detected in paired CSF, plasma, and urine samples of 11 acquired immunodeficiency syndrome (AIDS) patients affected by PML to try to determine where the rearranged JCV TCRs are selected. In one patient, it was also possible to amplify and sequence the TCR in the brain and lymphocytes. Moreover, in 5/11 patients, the CSF, plasma, and urine samples corresponding to 2 months after PML development were available; and in another patient, it was possible to sequence the TCR in plasma and lymphocytes sampled 8 months before the onset of PML. The presence of the same TCR sequences in all the CSF and plasma samples taken from individual patients could strengthen the hypothesis that the blood is a compartment where JCV may replicate and undergo rearrangement of the TCR. This further supports the hypothesis that JCV reaches the brain by a hematogenous route and indicates that the JCV TCR sequences detected in plasma could be used as an early marker of JCV pathogenicity before the clinical appearance of PML in immunocompromised patients
Cg-TIMP, an inducible tissue inhibitor of metalloproteinase from the Pacific oyster Crassostrea gigas with a potential role in wound healing and defense mechanisms(1)
No full textWe have cloned and characterized a cDNA encoding Cg-TIMP, the first tissue inhibitor of metalloproteinase identified in mollusks. The isolated cDNA encodes a protein of 221 residues that has a domain organization similar to that of vertebrate TIMPs including a signal sequence, and the 12 cysteines characteristic of the TIMP signature. Analysis of Cg-TIMP expression in adult oyster tissues, by Northern blot and in situ hybridization, indicates that Cg-TIMP was only expressed in hemocytes which are the key components of defense mechanisms in mollusks. We also observed that Cg-TIMP mRNA accumulated during shell damage and bacterial challenge. This pattern of expression suggests that Cg-TIMP may be an important factor in wound healing and defense mechanisms.LR: 20061115; PUBM: Print; GENBANK/AF321279; JID: 0155157; 0 (DNA, Complementary); 0 (RNA, Messenger); 0 (TIMP protein, Crassostrea gigas); 0 (Tissue Inhibitor of Metalloproteinases); ppublishSource type: Electronic(1
Subwavelength spinning of particles in vector cosine-Gaussian field with radial polarization
No full textA new type of radially polarized (RP) cosine-Gaussian (CG) field is proposed. Through the analytical model, it is found that such RP CG beam exhibits completely different focusing properties from the reported RP plane waves. More importantly, a stable three-dimensional trap of Rayleigh particle accompanied by a subwavelength spin motion can be easily achieved using this RP CG beam.Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.ImPhys/Optic
Het effect van een anisotropiecoëfficiënt in de Poissonvergelijking op de convergentie van de CG-methode en de ICCG(0)-methode
No full textAllerlei diffusieverschijnselen in de natuurkunde kunnen omschreven wordenmet de Poissonvergelijking op een gebied met te kiezen randvoorwaarden. Er zijn echter ook verschijnselen waarin er een gelaagdheid optreedt zodat er in verticalerichting minder makkelijk diffusie kan plaatsvinden. Dit leidt tot een vergelijkingmet toevoeging van een anisotropiecoëfficiënt epsilon, die dicht bij 0 ligt.Via (onder andere) de Finite Volume Method kunnen deze vergelijkingengediscretiseerd worden, wat leidt tot een stelsel Au = f. Hierbij is A symmetrischen positief deniet (alle eigenwaarden zijn positief). Er zijn tallozemethoden om dit stelsel op te lossen. Een hiervan is de CG-methode, eeniteratieve methode, met als uitbreiding de ICCG(0)-methode. De convergentievan de CG-methode blijkt af te hangen van de eigenwaarden van dematrix A. Hoe dichter de eigenwaarden bij elkaar liggen, hoe sneller deconvergentie. De geschaalde eigenwaarden1 van A liggen min of meer geconcentreerdrond 1. Het is voor een snelle convergentie van belang dat dekleinste eigenwaarden niet al te dicht bij 0 liggen. Dit leidt namelijk tottrage convergentie. Er zijn manieren om de eigenwaarden dichter bij elkaarte brengen. We noemen dat preconditionering. De ICCG(0)-methode is eenvorm van preconditionering en zorgt er (onder andere) voor dat de kleinsteeigenwaarden dichter bij 1 komen te liggen. In dit onderzoek wordt onderzochtwat er gebeurt met de eigenwaarden, zowel in de CG-methode als inde ICCG(0)-methode, als de anisotropiecoëfficiënt heel klein wordt. Hetblijkt dat de ondergrens voor de eigenwaarden van A lineair afhankelijk isvan epsilon. Dit leidt tot een zeer trage convergentie van de CG-methode in hetgeval epsilon klein is. Er blijkt echter ook dat preconditionering met behulp vande ICCG(0)-methode voldoende is om de ondergrens voor de eigenwaardenonafhankelijk te maken van epsilon. Dit betekent dat ook in situaties waarinanisotropie optreedt, ICCG(0) een geschikte methode is om de vergelijkingAu = f op te lossen
Effectiveness of using call graphs to detect propagated vulnerabilities
No full textNowadays software development greatly relies upon using third-party source code. A logical consequence is that vulnerabilities from such sources can be propagated to applications making use of those. Tools like Dependabot can alert developers about packages they use, which entail vulnerabilities. Such alerts oftentimes turn out to be false positives because the vulnerable functionality of the package is not used. Current research by the FASTEN Project revolves around analysing dependency networks using a finer granularity; moving from package-level to method-level analysis with the help of call graphs. Such analysis can theoretically be used to gain better insights into how vulnerable a dependency for an application is. This report aims to display the practical effectiveness of using call graphs to detect propagated vulnerabilities. To evaluate the effectiveness, results generated through method-level analysis were studied with regards to whether a vulnerability in the corresponding project is reproducible. Furthermore, possible improvements to call graphs to detect vulnerabilities more accurately are described in this study. An experiment, based on call graph analysis, was conducted to detect propagated vulnerabilities in a set of public software repositories. The used data about the repositories and vulnerabilities was provided by the FASTEN Project. Each vulnerability detection was manually verified and studied on its impact based on public information about the corresponding vulnerability. The results of this experiment show that none of the potential propagated vulnerabilities could be reproduced. This implies that a greater set of repositories needs to be analysed to draw meaningful conclusions for the effectiveness of call graphs to detect propagated vulnerabilities. The proposed improvements to call graphs display a fraction of the great potential of the precision that could be reached through such fine-grained analysis.https://github.com/jakub014/CG-dependency-analyzer The codebase for the experiment conducted in this study.CSE3000 Research ProjectComputer Science and Engineerin
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