| 41. |
- Ghannoum, S., et al.
(författare)
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DIscBIO: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics
- 2021
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Ingår i: International Journal of Molecular Sciences. - : MDPI AG. - 1422-0067. ; 22:3
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Tidskriftsartikel (refereegranskat)abstract
- The growing attention toward the benefits of single-cell RNA sequencing (scRNA-seq) is leading to a myriad of computational packages for the analysis of different aspects of scRNA-seq data. For researchers without advanced programing skills, it is very challenging to combine several packages in order to perform the desired analysis in a simple and reproducible way. Here we present DIscBIO, an open-source, multi-algorithmic pipeline for easy, efficient and reproducible analysis of cellular sub-populations at the transcriptomic level. The pipeline integrates multiple scRNA-seq packages and allows biomarker discovery with decision trees and gene enrichment analysis in a network context using single-cell sequencing read counts through clustering and differential analysis. DIscBIO is freely available as an R package. It can be run either in command-line mode or through a user-friendly computational pipeline using Jupyter notebooks. We showcase all pipeline features using two scRNA-seq datasets. The first dataset consists of circulating tumor cells from patients with breast cancer. The second one is a cell cycle regulation dataset in myxoid liposarcoma. All analyses are available as notebooks that integrate in a sequential narrative R code with explanatory text and output data and images. R users can use the notebooks to understand the different steps of the pipeline and will guide them to explore their scRNA-seq data. We also provide a cloud version using Binder that allows the execution of the pipeline without the need of downloading R, Jupyter or any of the packages used by the pipeline. The cloud version can serve as a tutorial for training purposes, especially for those that are not R users or have limited programing skills. However, in order to do meaningful scRNA-seq analyses, all users will need to understand the implemented methods and their possible options and limitations.
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| 42. |
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| 43. |
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| 44. |
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| 45. |
- Vardavas, CI, et al.
(författare)
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The independent role of prenatal and postnatal exposure to active and passive smoking on the development of early wheeze in children
- 2016
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Ingår i: The European respiratory journal. - : European Respiratory Society (ERS). - 1399-3003 .- 0903-1936. ; 48:1, s. 115-124
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Tidskriftsartikel (refereegranskat)abstract
- Maternal smoking during pregnancy increases childhood asthma risk, but health effects in children of nonsmoking mothers passively exposed to tobacco smoke during pregnancy are unclear. We examined the association of maternal passive smoking during pregnancy and wheeze in children aged ≤2 years.Individual data of 27 993 mother–child pairs from 15 European birth cohorts were combined in pooled analyses taking into consideration potential confounders.Children with maternal exposure to passive smoking during pregnancy and no other smoking exposure were more likely to develop wheeze up to the age of 2 years (OR 1.11, 95% CI 1.03–1.20) compared with unexposed children. Risk of wheeze was further increased by children's postnatal passive smoke exposure in addition to their mothers' passive exposure during pregnancy (OR 1.29, 95% CI 1.19–1.40) and highest in children with both sources of passive exposure and mothers who smoked actively during pregnancy (OR 1.73, 95% CI 1.59–1.88). Risk of wheeze associated with tobacco smoke exposure was higher in children with an allergic versus nonallergic family history.Maternal passive smoking exposure during pregnancy is an independent risk factor for wheeze in children up to the age of 2 years. Pregnant females should avoid active and passive exposure to tobacco smoke for the benefit of their children's health.
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| 46. |
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| 47. |
- Hohmann, C, et al.
(författare)
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The development of the MeDALL Core Questionnaires for a harmonized follow-up assessment of eleven European birth cohorts on asthma and allergies
- 2014
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Ingår i: International archives of allergy and immunology. - : S. Karger AG. - 1423-0097 .- 1018-2438. ; 163:3, s. 215-224
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Tidskriftsartikel (refereegranskat)abstract
- <b><i>Background:</i></b> Numerous birth cohorts have been initiated in the world over the past 30 years using heterogeneous methods to assess the incidence, course and risk factors of asthma and allergies. The aim of the present work is to provide the stepwise proceedings of the development and current version of the harmonized MeDALL-Core Questionnaire (MeDALL-CQ) used prospectively in 11 European birth cohorts. <b><i>Methods:</i></b> The harmonization of questions was accomplished in 4 steps: (i) collection of variables from 14 birth cohorts, (ii) consensus on questionnaire items, (iii) translation and back-translation of the harmonized English MeDALL-CQ into 8 other languages and (iv) implementation of the harmonized follow-up. <b><i>Results:</i></b> Three harmonized MeDALL-CQs (2 for parents of children aged 4-9 and 14-18, 1 for adolescents aged 14-18) were developed and used for a harmonized follow-up assessment of 11 European birth cohorts on asthma and allergies with over 13,000 children. <b><i>Conclusions:</i></b> The harmonized MeDALL follow-up produced more comparable data across different cohorts and countries in Europe and will offer the possibility to verify results of former cohort analyses. Thus, MeDALL can become the starting point to stringently plan, conduct and support future common asthma and allergy research initiatives in Europe.
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| 48. |
- Pateromichelakis, E., et al.
(författare)
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Interference Management Enablers for 5G Radio Access Networks
- 2016
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Ingår i: 2016 IEEE CONFERENCE ON STANDARDS FOR COMMUNICATIONS AND NETWORKING (CSCN). - : IEEE. - 9781509038626
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Konferensbidrag (refereegranskat)abstract
- Inter-cell interference can be seen as a huge challenge towards meeting the high capacity and coverage targets, as envisioned in 5G era. To this end, factors like the expected high density of access nodes reusing the same spectrum, the diverse sources of interference from heterogeneous access technologies, flexible wireless backhauling and the consideration of multiple 5G services with different KPIs can have strong impact on the way interference management is handled. This paper discusses three key interference management drivers, as good candidates for service-tailored optimization, which aimed improving users' performance in terms of cell-edge throughput, providing energy-efficiency aware resource management and minimizing the signalling overhead using BS clustering and context-awareness.
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| 49. |
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