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- Abel, Olubunmi, et al.
(författare)
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ALSoD : A user-friendly online bioinformatics tool for amyotrophic lateral sclerosis genetics
- 2012
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Ingår i: Human Mutation. - Hoboken, NJ : Wiley-Blackwell. - 1059-7794 .- 1098-1004. ; 33:9, s. 1345-1351
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Tidskriftsartikel (refereegranskat)abstract
- Amyotrophic lateral sclerosis (ALS) is the commonest adult onset motor neuron disease, with a peak age of onset in the seventh decade. With advances in genetic technology, there is an enormous increase in the volume of genetic data produced, and a corresponding need for storage, analysis, and interpretation, particularly as our understanding of the relationships between genotype and phenotype mature. Here, we present a system to enable this in the form of the ALS Online Database (ALSoD at http://alsod.iop.kcl.ac.uk), a freely available database that has been transformed from a single gene storage facility recording mutations in the SOD1 gene to a multigene ALS bioinformatics repository and analytical instrument combining genotype, phenotype, and geographical information with associated analysis tools. These include a comparison tool to evaluate genes side by side or jointly with user configurable features, a pathogenicity prediction tool using a combination of computational approaches to distinguish variants with nonfunctional characteristics from disease-associated mutations with more dangerous consequences, and a credibility tool to enable ALS researchers to objectively assess the evidence for gene causation in ALS. Furthermore, integration of external tools, systems for feedback, annotation by users, and two-way links to collaborators hosting complementary databases further enhance the functionality of ALSoD. Hum Mutat 33:1345-1351, 2012. (c) 2012 Wiley Periodicals, Inc.
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- Abel, Olubunmi, et al.
(författare)
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Credibility analysis of putative disease-causing genes using bioinformatics
- 2013
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:6, s. e64899-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Genetic studies are challenging in many complex diseases, particularly those with limited diagnostic certainty, low prevalence or of old age. The result is that genes may be reported as disease-causing with varying levels of evidence, and in some cases, the data may be so limited as to be indistinguishable from chance findings. When there are large numbers of such genes, an objective method for ranking the evidence is useful. Using the neurodegenerative and complex disease amyotrophic lateral sclerosis (ALS) as a model, and the disease-specific database ALSoD, the objective is to develop a method using publicly available data to generate a credibility score for putative disease-causing genes.Methods: Genes with at least one publication suggesting involvement in adult onset familial ALS were collated following an exhaustive literature search. SQL was used to generate a score by extracting information from the publications and combined with a pathogenicity analysis using bioinformatics tools. The resulting score allowed us to rank genes in order of credibility. To validate the method, we compared the objective ranking with a rank generated by ALS genetics experts. Spearman's Rho was used to compare rankings generated by the different methods.Results: The automated method ranked ALS genes in the following order: SOD1, TARDBP, FUS, ANG, SPG11, NEFH, OPTN, ALS2, SETX, FIG4, VAPB, DCTN1, TAF15, VCP, DAO. This compared very well to the ranking of ALS genetics experts, with Spearman's Rho of 0.69 (P = 0.009).Conclusion: We have presented an automated method for scoring the level of evidence for a gene being disease-causing. In developing the method we have used the model disease ALS, but it could equally be applied to any disease in which there is genotypic uncertainty.
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- Abel, Olubunmi, et al.
(författare)
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Development of a Smartphone App for a Genetics Website : The Amyotrophic Lateral Sclerosis Online Genetics Database (ALSoD)
- 2013
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Ingår i: JMIR mhealth and uhealth. - : JMIR Publications, Inc.. - 2291-5222. ; 1:2
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Tidskriftsartikel (refereegranskat)abstract
- Background: The ALS Online Genetics Database (ALSoD) website holds mutation, geographical, and phenotype data on genes implicated in amyotrophic lateral sclerosis (ALS) and links to bioinformatics resources, publications, and tools for analysis. On average, there are 300 unique visits per day, suggesting a high demand from the research community. To enable wider access, we developed a mobile-friendly version of the website and a smartphone app. Objective: We sought to compare data traffic before and after implementation of a mobile version of the website to assess utility. Methods: We identified the most frequently viewed pages using Google Analytics and our in-house analytic monitoring. For these, we optimized the content layout of the screen, reduced image sizes, and summarized available information. We used the Microsoft. NET framework mobile detection property (HttpRequest. IsMobileDevice in the Request. Browser object in conjunction with HttpRequest. UserAgent), which returns a true value if the browser is a recognized mobile device. For app development, we used the Eclipse integrated development environment with Android plug-ins. We wrapped the mobile website version with the WebView object in Android. Simulators were downloaded to test and debug the applications. Results: The website automatically detects access from a mobile phone and redirects pages to fit the smaller screen. Because the amount of data stored on ALSoD is very large, the available information for display using smartphone access is deliberately restricted to improve usability. Visits to the website increased from 2231 to 2820, yielding a 26% increase from the pre-mobile to post-mobile period and an increase from 103 to 340 visits (230%) using mobile devices (including tablets). The smartphone app is currently available on BlackBerry and Android devices and will be available shortly on iOS as well. Conclusions: Further development of the ALSoD website has allowed access through smartphones and tablets, either through the website or directly through a mobile app, making genetic data stored on the database readily accessible to researchers and patients across multiple devices.
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- Ammar, F., et al.
(författare)
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Ternary q-Virasoro-Witt Hom-Nambu-Lie algebras
- 2010
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Ingår i: Journal of Physics A. - : IOP Publishing. - 1751-8113 .- 1751-8121. ; 43:26, s. 265204-
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Tidskriftsartikel (refereegranskat)abstract
- In this paper we construct ternary q-Virasoro-Witt algebras which q-deform the ternary Virasoro-Witt algebras constructed by Curtright, Fairlie and Zachos using su(1, 1) enveloping algebra techniques. The ternary Virasoro-Witt algebras constructed by Curtright, Fairlie and Zachos depend on a parameter and are not Nambu-Lie algebras for all but finitely many values of this parameter. For the parameter values for which the ternary Virasoro-Witt algebras are Nambu-Lie, the corresponding ternary q-Virasoro-Witt algebras constructed in this paper are also Hom-Nambu-Lie because they are obtained from the ternary Nambu-Lie algebras using the composition method. For other parameter values this composition method does not yield a Hom-Nambu-Lie algebra structure for q-Virasoro-Witt algebras. We show however, using a different construction, that the ternary Virasoro-Witt algebras of Curtright, Fairlie and Zachos, as well as the general ternary q-Virasoro-Witt algebras we construct, carry a structure of the ternary Hom-Nambu-Lie algebra for all values of the involved parameters.
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- Dickinson, S., et al.
(författare)
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Experimental and modelling studies of iodine oxide formation and aerosol behaviour relevant to nuclear reactor accidents
- 2014
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Ingår i: Annals of Nuclear Energy. - : Elsevier BV. - 0306-4549 .- 1873-2100. ; 74, s. 200-207
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Tidskriftsartikel (refereegranskat)abstract
- Plant assessments have shown that iodine contributes significantly to the source term for a range of accident scenarios. Iodine has a complex chemistry that determines its chemical form and, consequently, its volatility in the containment. If volatile iodine species are formed by reactions in the containment, they will be subject to radiolytic reactions in the atmosphere, resulting in the conversion of the gaseous species into involatile iodine oxides, which may deposit on surfaces or re-dissolve in water pools. The concentration of airborne iodine in the containment will, therefore, be determined by the balance between the reactions contributing to the formation and destruction of volatile species, as well as by the physicochemical properties of the iodine oxide aerosols which will influence their longevity in the atmosphere. This paper summarises the work that has been done in the framework of the EC SARNET (Severe Accident Research Network) to develop a greater understanding of the reactions of gaseous iodine species in irradiated air/steam atmospheres, and the nature and behaviour of the reaction products. This work has mainly been focussed on investigating the nature and behaviour of iodine oxide aerosols, but earlier work by members of the SARNET group on gaseous reaction rates is also discussed to place the more recent work into context.
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- Khayat, Kamal H., et al.
(författare)
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Field-oriented test methods to evaluate structural build-up at rest of flowable mortar and concrete
- 2012
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Ingår i: Materials and Structures. - : Springer Science and Business Media LLC. - 1359-5997 .- 1871-6873. ; 45:10, s. 1547-1564
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Tidskriftsartikel (refereegranskat)abstract
- Thixotropy of flowable mortar and concrete is an important property that affects stability and form pressure characteristics. The increase in thixotropy can reduce lateral pressure on formwork systems. On the other hand, low thixotropy or a continuous casting is required to eliminate the formation of weak interface between lifts in multilayer casting. Thixotropy can be assessed by determining the rate of structural build-up at rest, which necessitates the use of simple and robust test methods to be quantified. Five field-oriented test methods that can be used for the determination of structural build-up at rest of mortar and concrete are proposed in this paper in an attempt to select a reliable field-oriented test. This includes the inclined plane (IP), portable vane (PV), undisturbed slump spread (USS), cone penetration (CP), and K-slump test methods. The repeatability of these test methods was determined four times using two concrete-equivalent mortars and two self-consolidating concretes (SCC) of different thixotropy levels. The IP, PV, and USS tests showed relative error (RE) values of 0.5-37 %. The CP test was successfully used to determine structural build-up of mortar; however, it was difficult to assess the thixotropy of concrete. The K-slump test exhibited a RE, less than 12 % for SCC mixtures with low thixotropy, but up to 76 % for highly thixotropic SCC. Good correlations were established among the various structural build-up indices determined from the proposed test methods and those determined by rheometric tests using various concrete.
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| 10. |
- Shatunov, Aleksey, et al.
(författare)
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Chromosome 9p21 in sporadic amyotrophic lateral sclerosis in the UK and seven other countries : a genome-wide association study
- 2010
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Ingår i: Lancet Neurology. - 1474-4422 .- 1474-4465. ; 9:10, s. 986-994
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Tidskriftsartikel (refereegranskat)abstract
- We have found strong evidence of a genetic association of two single nucleotide polymorphisms on chromosome 9 with sporadic ALS, in line with findings from previous independent GWAS of ALS and linkage studies of ALS-frontotemporal dementia. Our findings together with these earlier findings suggest that genetic variation at this locus on chromosome 9 causes sporadic ALS and familial ALS-frontotemporal dementia. Resequencing studies and then functional analysis should be done to identify the defective gene.
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