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Articles by van Dorp
Quantitative Biology > Quantitative Methods
Transit compartment models are widely used in pharmacokinetics/pharmacodynamics to represent delayed biological processes such as absorption, maturation, cellular proliferation, and treatment-induced toxicity. This transit compartment formulation imposes an artificial relationship between the mean and variance of the delay distribution, as the number of transit compartment must be integer-valued number of transit compartments.
Detection of a historic reservoir of bedaquiline/clofazimine resistance-associated variants in Mycobacterium tuberculosis - Genome Medicine
To investigate the global distribution of Mtb isolates with variants in mmpR5, we curated two large datasets of whole genomes from the two dominant global lineages L2 and L4. Both datasets were enriched for samples with variants in mmpR5 following a screen for variants in public sequencing repositories (see Methods) and retaining those samples uploaded with accompanying full metadata for geolocation and time of sampling (Fig. 1, Additional file 1: Table S1, Additional file 2: Fig S1, Table S2).
The prevalence of thyroid dysfunction and hyperprolactinemia in women with PCOS
Introduction An irregular or absent menstrual cycle, also known as ovulatory dysfunction, is a common cause of subfertility in women of reproductive age. Ovulatory dysfunction is usually caused by an endocrine disorder, of which polycystic ovary syndrome (PCOS) is the most common cause. The prevalence of PCOS has been estimated at 4-21%, according to the Rotterdam Criteria (1).
The bladder cancer immune micro-environment in the context of response to immune checkpoint inhibition
Introduction Urothelial carcinoma of the bladder, more commonly described as bladder cancer (BC), is the 10th most common cancer worldwide (1, 2). In approximately 25% of BC cases, patients present with muscle-invasive disease, characterized by invasion of tumor cells into the muscularis propria layer of the urothelium. Standard treatment for muscle-invasive bladder cancer (MIBC) consists of radical cystectomy (RC) including removal of the locoregional lymph nodes (3–5).
Population structure and hybridisation in a population of Hawaiian feral chickens
Heredity, Feb 2023 This is a preview of a remote PDF: https://www.nature.com/articles/s41437-022-00589-z.pdf Martin Cerezo, Maria Luisa, López, Saioa, van Dorp, Lucy, Hellenthal, Garrett, Johnsson, Martin, Gering, Eben, Henriksen, Rie, Wright, Dominic. , Heredity, DOI: 10.1038/s41437-022-00589-z
The past, current and future epidemiological dynamic of SARS-CoV-2
Zenodo DOI Badge DOI 10.5281/zenodo.6402144 Markdown [](https://doi.org/10.5281/zenodo.6402144) reStructedText ..
Role of mobile genetic elements in the global dissemination of the carbapenem resistance gene blaNDM - Nature Communications
Abstract The mobile resistance gene blaNDM encodes the NDM enzyme which hydrolyses carbapenems, a class of antibiotics used to treat some of the most severe bacterial infections. The blaNDM gene is globally distributed across a variety of Gram-negative bacteria on multiple plasmids, typically located within highly recombining and transposon-rich genomic regions, which leads to the dynamics underlying the global dissemination of blaNDM to remain poorly resolved.
Drivers of methicillin-resistant Staphylococcus aureus (MRSA) lineage replacement in China - Genome Medicine
Hongbin Chen1,2 na1, Yuyao Yin1 na1, Lucy van Dorp2 na1, Liam P. Shaw2,3, Hua Gao1, Mislav Acman2, Jizhen Yuan1,5, Fengning Chen1, Shijun Sun1, Xiaojuan Wang1, Shuguang Li1, Yawei Zhang1, Rhys A. Farrer2,4, Hui Wang ORCID: orcid.org/0000-0001-9220-03571 & Francois Balloux2 Genome Medicine volume 13, Article number: 171 (2021) Cite this article Abstract Background Methicillin-resistant Staphylococcus aureus (MRSA) is a major nosocomial pathogen subdivided into lineages termed sequence types (STs).
A participant-derived xenograft model of HIV enables long-term evaluation of autologous immunotherapies
Skip Nav Destination Technical Advances and Resources| May 14 2021 You do not currently have access to this content. Sign in Client Account You could not be signed in. Please check your email address / username and password and try again. Email address / Username ? Password
Widespread genetic connectivity of feral pigeons across the Northeastern megacity
Abstract Urbanization may restrict, facilitate, or have no effect on gene flow, depending on the organism and extent of urbanization. In human commensals, with high dispersal ability, urbanization can facilitate gene flow by providing continuous suitable habitat across a wide range. Additionally, suburban or rural areas with lower human population density may act as a barrier to gene flow for these human commensals.
River piracy and drainage basin reorganization led by climate-driven glacier retreat
1. Bates, R. L. & Jackson, J. A. Dictionary of geological terms. Am. Geol. Inst.386 (1984). 2. Willett, S. D., McCoy, S. W., Perron, J. T., Goren, L. & Chen, C. Y. Dynamic reorganization of river basins. Science 343, 1248765 (2014). 3. Bishop, P. Drainage rearrangement by river capture, beheading and diversion. Prog. Phys. Geogr. 19, 449–473 (1995). 4. Vella, P., Neef, G. & Kaewyana, W. River piracy at Kakariki, north-western Wairarapa, New Zealand. J. R. Soc. N.Z. 17, 373–380 (1987). 5. Carter, S. P., Fricker, H. A.
The Genetic Legacy of State Centralization in the Kuba Kingdom of the Democratic Republic of the Congo
Hellenthal, GR; van Dorp, L; Thomas, M; Lopez, S; Mendoza-Revilla, J; (2019) The Genetic Legacy of State Centralization in the Kuba Kingdom of the Democratic Republic of the Congo. Proceedings of the National Academy of Sciences (In press). Text (Article) Hellenthal_Kuba_paper_final_response_accept_changes.pdf - ["content_typename_Accepted version" not defined] Access restricted to UCL open access staff until 12 June 2019.
From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic
Balloux, F; Brønstad Brynildsrud, O; van Dorp, L; Shaw, LP; Chen, H; Harris, KA; Wang, H; Balloux, F; Brønstad Brynildsrud, O; van Dorp, L; Shaw, LP; Chen, H; Harris, KA; Wang, H; Eldholm, V; - view fewer (2018) From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic. Trends in Microbiology , 26 (12) pp. 1035-1048. 10.1016/j.tim.2018.08.004.
A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots - Nature Communications
Abstract Genetic clustering algorithms, implemented in programs such as STRUCTURE and ADMIXTURE, have been used extensively in the characterisation of individuals and populations based on genetic data. A successful example is the reconstruction of the genetic history of African Americans as a product of recent admixture between highly differentiated populations.
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