| 1. |
- Alghamdi, Azza
(författare)
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Approximation of pluricomplex Green functions : A probabilistic approach
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This PhD thesis focuses on probabilistic methods of approximation of pluricomplex Green functions and is based on four papers.The thesis begins with a general introduction to the use of pluricomplex Green functions in multidimensional complex analysis and a review of their main properties. This is followed by short description of the main results obtained in the enclosed papers.In Paper I, we study properties of the metric space of pluriregular sets, that is zero sets of continuous pluricomplex Green functions. The best understood non-trivial examples of such sets are composite Julia sets, obtained by iteration of finite families of polynomial mappings in several complex variables. We prove that the so-called chaos game is applicable in the case of such sets. We also visualize some composite Julia sets using escape time functions and Monte Carlo simulation.In Paper II, we extend results in Paper I to the case of infinite compact families of proper polynomials mappings. With composition as the semigroup operation, we generate families of infinite iterated function systems with compact attractors. We show that such attractors can be approximated probabilistically in a manner of the classic chaos game.In Paper III, we study numerical approximation and visualisation of pluricomplex Green functions based on the Monte-Carlo integration. Unlike alternative methods that rely on locating a sequence of carefully chosen finite sets of points satisfying some optimal conditions for approximation purposes, our approach is simpler and more direct by relying on generation of pseudorandom points. We examine numerically the errors of approximation for some simple geometric shapes for which the pluricomplex Green functions are known. If the pluricomplex Green functions are not known, the errors in Monte Carlo integration can be expressed with the aid of statistics in terms of confidence intervals.Finally, in Paper IV, we study how perturbations of an orthonomalization procedure influence the resulting approximate Bergman functions. To this end we consider the concept of near orthonormality of a finite set of vectors in an inner product space, understood as closeness of the Gram matrix of those vectors to the identity matrix. We provide estimates for the errors resulting from using nearly orthogonal bases instead of orthogonal ones. The motivation for this work comes from Paper III: when Gram matrices are calculated via Monte Carlo integration, the outcomes of standard orthogonalisation algorithms are nearly orthonormal bases.
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| 2. |
- Alghamdi, Azza, et al.
(författare)
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Attractors of compactly generated semigroups of regular polynomial mappings.
- 2018
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Ingår i: Complexity. - : Hindawi Limited. - 1076-2787 .- 1099-0526.
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Tidskriftsartikel (refereegranskat)abstract
- We investigate the metric space of pluriregular sets as well as the contractions on that space induced by infinite compact families of proper polynomial mappings of several complex variables. The topological semigroups generated by such families, with composition as the semigroup operation, lead to the constructions of a variety of Julia-type pluriregular sets. The generating families can also be viewed as infinite iterated function systems with compact attractors. We show that such attractors can be approximated both deterministically and probabilistically in a manner of the classic chaos game.
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| 3. |
- Alghamdi, Azza, et al.
(författare)
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Probabilistic approximation of partly filled-in composite Julia sets
- 2017
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Ingår i: Annales Polonici Mathematici. - : Institute of Mathematics, Polish Academy of Sciences. - 0066-2216 .- 1730-6272. ; 119:3, s. 203-220
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Tidskriftsartikel (refereegranskat)abstract
- We study properties of the metric space of pluriregular sets and of contractions on that space induced by finite families of proper polynomial mappings of several complex variables. In particular, we show that closed balls in the space of pluriregular sets do not have to be compact and we give a simple proof of applicability of the so-called chaos game in the case of composite Julia sets. Part of the construction of those sets also leads to a computationally viable approximation by simpler sets based on Monte-Carlo simulation.
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| 4. |
- Chapman, Lesley M, et al.
(författare)
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SVCurator: A Crowdsourcing app to visualize evidence of structural variants for the human genome
- 2019
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- A high quality benchmark for small variants encompassing 88 to 90% of the reference genome has been developed for seven Genome in a Bottle (GIAB) reference samples. However a reliable benchmark for large indels and structural variants (SVs) is yet to be defined. In this study, we manually curated 1235 SVs which can ultimately be used to evaluate SV callers ortrain machine learning models. We developed a crowdsourcing app - SVCurator - to help curators manually review large indels and SVs within the human genome, and report their genotype and size accuracy.SVCurator is a Python Flask-based web platform that displays images from short, long, and linked read sequencing data from the GIAB Ashkenazi Jewish Trio son [NIST RM 8391/HG002]. We asked curators to assign labels describing SV type (deletion or insertion), size accuracy, and genotype for 1235 putative insertions and deletions sampled from different size bins between 20 and 892,149 bp. The crowdsourced results were highly concordant with 37 out ofthe 61 curators having at least 78% concordance with a set of ‘expert’ curators, where there was 93% concordance amongst ‘expert’ curators. This produced high confidence labels for 935 events. When compared to the heuristic-based draft benchmark SV callset from GIAB, the SVCurator crowdsourced labels were 94.5% concordant with the benchmark set. We found that curators can successfully evaluate putative SVs when given evidence from multiple sequencing technologies.
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| 5. |
- El-Sayed, Ashraf S. A., et al.
(författare)
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Aspergillus nidulans thermostable arginine deiminase-Dextran conjugates with enhanced molecular stability, proteolytic resistance, pharmacokinetic properties and anticancer activity
- 2019
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Ingår i: Enzyme and microbial technology. - : Elsevier. - 0141-0229 .- 1879-0909. ; 131
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Tidskriftsartikel (refereegranskat)abstract
- The potential anticancer activity of arginine deiminase (ADI) via deimination of L-arginine into citrulline has been extensively verified against various arginine-auxotrophic tumors, however, the higher antigenicity, structural instability and in vivo proteolysis are the major challenges that limit this enzyme from further clinical implementation. Since, this clinically applied enzyme was derived from Mycobacterium spp, thus, searching for ADI from eukaryotic microbes "especially thermophilic fungi" could have a novel biochemical conformational and catalytic properties. Aspergillus nidulans ADI was purified with 5.3 folds, with molecular subunit structure 48 kDa and entire molecular mass 120 kDa, ensuring its homotrimeric identity. The peptide fingerprinting analysis revealing the domain Glu(95)-Gly(96)-Gly(97) as the conserved active site of A. nidulans ADI, with higher proximity to Mycobacterium ADI Glade IV. In an endeavor to fortify the structural stability and anticancer activity of A. nidulans ADI, the enzyme was chemically modified with dextran. The optimal activity of Dextran-ADI conjugates was determined at 0.08:20 M ratio of ADI: Dextran, with an overall increase to ADI molecular subunit mass to (similar to)100 kDa. ADI was conjugated with dextran via the a-amino groups interaction of surface lysine residues of ADI. The resistance of Dextran-ADI conjugate to proteolysis had been increased by 2.5 folds to proteinase K and trypsin, suggesting the shielding of > 50% of ADI surface proteolytic recognition sites. The native and Dextran-ADI conjugates have the same optimum reaction temperature (37 degrees C), reaction pH and pH stability (7.0-8.0) with dependency on K+ ions as a cofactor. Dextran-ADI conjugates exhibited a higher thermal stability by (similar to) 2 folds for all the tested temperatures, ensuring the acquired structural and catalytic stability upon dextran conjugation. Dextran conjugation slightly protect the reactive amino and thiols groups of surface amino acids of ADI from amino acids suicide inhibitors. The affinity of ADI was increased by 5.3 folds to free L-arginine with a dramatic reduction in citrullination of peptidylarginine residues upon dextran conjugation. The anticancer activity of ADI to breast (MCF-7), liver (HepG-2) and colon (HCTB, HT29, DLD1 and LS174 T) cancer cell lines was increased by 1.7 folds with dextran conjugation in vitro. Pharmacokinetically, the half-life time of ADI was increased by 1.7 folds upon dextran conjugation, in vivo. From the biochemical and hematological parameters, ADIs had no signs of toxicity to the experimental animals. In addition to the dramatic reduction of L-arginine in serum, citrulline level was increased by 2.5 folds upon dextran conjugation of ADI. This is first report exploring thermostable ADI from thermophilic A. nidulans with robust structural stability, catalytic efficiency and proteolytic resistance.
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| 6. |
- Kock, Ida Elin, et al.
(författare)
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Menneskelivet bak prostitusjonen
- 2015
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Ingår i: Tidsskrift for Den norske lægeforening. - 0029-2001 .- 0807-7096. ; 135:17, s. 1564-1566
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- I denne artikkelen vil vi gi et innblikk i noen av disse livene gjennom fiktive pasienthistorier basert på våre erfaringer med migrerte kvinner vi møter på Pro Sentret, en «drop in»-klinikk for personer som selger seksuelle tjenester i Oslo.Prostitusjonsmarkedet har det siste tiåret vært i stor forandring. Personene som brukte Pro Sentrets tilbud tidligere, var i hovedsak norske kvinner med rusproblematikk, men siden tidlig på 2000-tallet har antallet migrerte kvinner vokst eksplosjonsartet (1 – 3). I 2014 hadde 90 % av våre pasienter annen opprinnelse enn norsk (1). Denne forholdsvis raske forandringen har ført til at vi har tilpasset våre helsetjenester – for på best mulig måte å imøtekomme de særskilte behovene denne gruppen har. En utfordring i møtet med denne pasientgruppen finnes selvfølgelig i språket. Ofte har pasientene dårlige ferdigheter i både norsk og engelsk, og grunnet uforutsigbarheten – pasientene benytter seg vanligvis ikke av timebestilling – er det vanskelig å ha en tolk til stede. Vi er derfor mange ganger henvist til å bruke mimikk og kroppsspråk for å kommunisere. En større utfordring befinner seg i den sosiokulturelle sfæren, og det er fremfor alt den vi kommer til å berøre i denne artikkelen.
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