| 1. |
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| 2. |
- Kehoe, Laura, et al.
(författare)
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Make EU trade with Brazil sustainable
- 2019
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 364:6438, s. 341-
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 3. |
- Ostaszewski, Marek, et al.
(författare)
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COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms
- 2021
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Ingår i: Molecular Systems Biology. - : John Wiley & Sons. - 1744-4292 .- 1744-4292. ; 17:10
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Tidskriftsartikel (refereegranskat)abstract
- We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective.
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| 4. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 5. |
- Covaci, Adrian, et al.
(författare)
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Urinary BPA measurements in children and mothers from six European member states: Overall results and determinants of exposure.
- 2015
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Ingår i: Environmental Research. - : Elsevier BV. - 1096-0953 .- 0013-9351. ; 141:Oct 13, s. 77-85
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Tidskriftsartikel (refereegranskat)abstract
- For the first time in Europe, both European-wide and country-specific levels of urinary Bisphenol A (BPA) were obtained through a harmonized protocol for participant recruitment, sampling and quality controlled biomarker analysis in the frame of the twin projects COPHES and DEMOCOPHES. 674 child-mother pairs were recruited through schools or population registers from six European member states (Belgium, Denmark, Luxembourg, Slovenia, Spain and Sweden). Children (5-12y) and mothers donated a urine sample. Information on socio-demographic characteristics, life style, dietary habits, and educational level of the parents was provided by mothers. After exclusion of urine samples with creatinine values below 300mg/L or above 3000mg/L, 653 children and 639 mothers remained for which BPA was measured. The geometric mean (with 95% confidence intervals) and 90th percentile were calculated for BPA separately in children and in mothers and were named "European reference values". After adjustment for confounders (age and creatinine), average exposure values in each country were compared with the mean of the "European reference values" by means of a weighted analysis of variance. Overall geometric means of all countries (95% CI) adjusted for urinary creatinine, age and gender were 2.04 (1.87-2.24) µg/L and 1.88 (1.71-2.07) µg/L for children (n=653) and mothers (n=639), respectively. Multiple regression analysis was used to identify significant environmental, geographical, personal or life style related determinants. Consumption of canned food and social class (represented by the highest educational level of the family) were the most important predictors for the urinary levels of BPA in mothers and children. The individual BPA levels in children were significantly correlated with the levels in their mothers (r=0.265, p<0.001), which may suggest a possible common environmental/dietary factor that influences the biomarker level in each pair. Exposure of the general European population was well below the current health-based guidance values and no participant had BPA values higher than the health-based guidance values.
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| 6. |
- Fresard, Laure, et al.
(författare)
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Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts
- 2019
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Ingår i: Nature Medicine. - : NATURE PUBLISHING GROUP. - 1078-8956 .- 1546-170X. ; 25:6, s. 911-919
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Tidskriftsartikel (refereegranskat)abstract
- It is estimated that 350 million individuals worldwide suffer from rare diseases, which are predominantly caused by mutation in a single gene(1). The current molecular diagnostic rate is estimated at 50%, with whole-exome sequencing (WES) among the most successful approaches(2-5). For patients in whom WES is uninformative, RNA sequencing (RNA-seq) has shown diagnostic utility in specific tissues and diseases(6-8). This includes muscle biopsies from patients with undiagnosed rare muscle disorders(6,9), and cultured fibroblasts from patients with mitochondrial disorders(7). However, for many individuals, biopsies are not performed for clinical care, and tissues are difficult to access. We sought to assess the utility of RNA-seq from blood as a diagnostic tool for rare diseases of different pathophysiologies. We generated whole-blood RNA-seq from 94 individuals with undiagnosed rare diseases spanning 16 diverse disease categories. We developed a robust approach to compare data from these individuals with large sets of RNA-seq data for controls (n = 1,594 unrelated controls and n = 49 family members) and demonstrated the impacts of expression, splicing, gene and variant filtering strategies on disease gene identification. Across our cohort, we observed that RNA-seq yields a 7.5% diagnostic rate, and an additional 16.7% with improved candidate gene resolution.
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| 7. |
- Hernández García, Daniel, et al.
(författare)
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Social Robots in Therapy and Care
- 2019
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Ingår i: Proceedings of the 14th ACM/IEEE International Conference on Human Robot Interaction. - Daegu : IEEE conference proceedings. - 9781538685556 - 9781538685563 - 9781538685549 ; , s. 669-670
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Konferensbidrag (refereegranskat)abstract
- The Social Robots in Therapy workshop series aims at advancing research topics related to the use of robots in the contexts of Social Care and Robot-Assisted Therapy (RAT). Robots in social care and therapy have been a long time promise in HRI as they have the opportunity to improve patients life significantly. Multiple challenges have to be addressed for this, such as building platforms that work in proximity with patients, therapists and health-care professionals; understanding user needs; developing adaptive and autonomous robot interactions; and addressing ethical questions regarding the use of robots with a vulnerable population. The full-day workshop follows last year's edition which centered on how social robots can improve health-care interventions, how increasing the degree of autonomy of the robots might affect therapies, and how to overcome the ethical challenges inherent to the use of robot assisted technologies. This 2nd edition of the workshop will be focused on the importance of equipping social robots with socio-emotional intelligence and the ability to perform meaningful and personalized interactions. This workshop aims to bring together researchers and industry experts in the fields of Human-Robot Interaction, Machine Learning and Robots in Health and Social Care. It will be an opportunity for all to share and discuss ideas, strategies and findings to guide the design and development of robot assisted systems for therapy and social care implementations that can provide personalize, natural, engaging and autonomous interactions with patients (and health-care providers).
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| 8. |
- Lai, De-Hua, et al.
(författare)
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Solanesyl Diphosphate Synthase, an Enzyme of the Ubiquinone Synthetic Pathway, Is Required throughout the Life Cycle of Trypanosoma brucei
- 2014
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Ingår i: Eukaryotic Cell. - 1535-9778 .- 1535-9786. ; 13:2, s. 320-328
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Tidskriftsartikel (refereegranskat)abstract
- Ubiquinone 9 (UQ9), the expected product of the long-chain solanesyl diphosphate synthase of Trypanosoma brucei (TbSPPS), has a central role in reoxidation of reducing equivalents in the mitochondrion of T. brucei. The ablation of TbSPPS gene expression by RNA interference increased the generation of reactive oxygen species and reduced cell growth and oxygen consumption. The addition of glycerol to the culture medium exacerbated the phenotype by blocking its endogenous generation and excretion. The participation of TbSPPS in UQ synthesis was further confirmed by growth rescue using UQ with 10 isoprenyl subunits (UQ10). Furthermore, the survival of infected mice was prolonged upon the downregulation of TbSPPS and/or the addition of glycerol to drinking water. TbSPPS is inhibited by 1-[(n-oct-1-ylamino)ethyl] 1,1-bisphosphonic acid, and treatment with this compound was lethal for the cells. The findings that both UQ9 and ATP pools were severely depleted by the drug and that exogenous UQ10 was able to fully rescue growth of the inhibited parasites strongly suggest that TbSPPS and UQ synthesis are the main targets of the drug. These two strategies highlight the importance of TbSPPS for T. brucei, justifying further efforts to validate it as a new drug target.
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| 9. |
- Martin-Lagarde, Marine, et al.
(författare)
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Magrathea : A proposal for a satellite mission on protoplanetary dust growth experiments
- 2018
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Ingår i: IAC-18. - : International Astronautical Federation.
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Konferensbidrag (refereegranskat)abstract
- The process of planet formation, from dust to protoplanetary disks, is not very well understood. The physics of both particle growth in protoplanetary disks and small particle dust gravity dynamics are well studied. However, the link between the two, i.e. the growth gap between dust grains and mm-sized particles, is still not understood. Additionally, current methods cannot model the full complexity of interactions in this phase of planet formation. Therefore, experiments in microgravity are crucial to revealing the underlying physics. Previous experiments have several limitations in particular their short duration and constrained dimensions. Accurately representing the conditions in the protoplanetary disk, such as the dust particle mean free path and large spatial extent of the dust, is very demanding, especially with larger, longer duration experiments.In order to create the best conditions for these experiments to be scientifically sound, with a reasonable solution, here we present a concept satellite with a 6 m3 chamber. The payload bay provides different measurements of ongoing collision processes, and samples of collision products. Its modularity and capacity is designed to carry several instruments in a carrousel, with 28 experiment canisters. Those experiments have a range of compositions (including silicates and Fayalite, both with or without ice layers), size distribution (between 1 µm and 100 mm), and shape properties, probing the conditions that could benefit grain growth. Each experiment will last up to one month allowing the record of approximately 106 collisions, with relative velocities of up to 5 mm/s, obtaining statistically meaningful results.With the science objectives and requirements formulated, payload solutions were prepared, and a conceptual mission and spacecraft design was developed. Considering the experiment phase will last up to 5 years, and during that time external influences should be minimised, the three most complex systems are the structure, thermal control, and attitude control. After several trade-offs and a cost analysis, a 1000 kg spacecraft solution was reached, set on a 800 km Sun-synchronous orbit. The mission would cost around 438 M Euros.The full work was developed during the 10 days of the 2017 Alpbach Summer School, by a group of fifteen young scientists and engineers, with various backgrounds, from all across Europe, with the support of two dedicated tutors. A concurrent engineering approach, with participants divided among several teams has been used to evaluate more than one scenario, and thus reach a concise solution.
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| 10. |
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