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| 2. |
- Kehoe, Laura, et al.
(author)
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Make EU trade with Brazil sustainable
- 2019
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 364:6438, s. 341-
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Journal article (other academic/artistic)
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| 3. |
- Touja, Justine, et al.
(author)
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Self-supported carbon nanofibers as negative electrodes for K-ion batteries: Performance and mechanism
- 2020
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In: Electrochimica Acta. - : Elsevier BV. - 0013-4686. ; 362
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Journal article (peer-reviewed)abstract
- Self-standing carbon nanofibers (CNF) were electrospun and tested in K-ion batteries (KIP). The comparison of the electrochemical performance of KIP using potassium bis(fluorosulfonyl)imide (KFSI) and potassium hexafluorophosphate (KPF6) carbonate-based electrolytes revealed that, despite the coulombic efficiency is more readily stabilized with KFSI than with KPF6, the long-term cycling is quite the same, with a specific capacity of 200 mAh.g(-1) for the CNF electrode. Post-mortem X-ray photoelectron spectroscopy analysis shows a more stable solid electrolyte interphase (SEI) for KIP employing KFSI. Finally, the K+ ion storage mechanism was investigated by combining cyclic voltammetry and operando Raman spectroscopy, showing a combination of adsorption and intercalation processes. The rate capability is, however, better with the KPF6 salt due to SEI layers formed at both CNF and K metal electrode, highlighting that full cell may lead to even superior results.
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| 4. |
- Ahmed, Laeeq
(author)
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Scalable Analysis of Large Datasets in Life Sciences
- 2019
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Doctoral thesis (other academic/artistic)abstract
- We are experiencing a deluge of data in all fields of scientific and business research, particularly in the life sciences, due to the development of better instrumentation and the rapid advancements that have occurred in information technology in recent times. There are major challenges when it comes to handling such large amounts of data. These range from the practicalities of managing these large volumes of data, to understanding the meaning and practical implications of the data.In this thesis, I present parallel methods to efficiently manage, process, analyse and visualize large sets of data from several life sciences fields at a rapid rate, while building and utilizing various machine learning techniques in a novel way. Most of the work is centred on applying the latest Big Data Analytics frameworks for creating efficient virtual screening strategies while working with large datasets. Virtual screening is a method in cheminformatics used for Drug discovery by searching large libraries of molecule structures. I also present a method for the analysis of large Electroencephalography data in real time. Electroencephalography is one of the main techniques used to measure the brain electrical activity.First, I evaluate the suitability of Spark, a parallel framework for large datasets, for performing parallel ligand-based virtual screening. As a case study, I classify molecular library using prebuilt classification models to filter out the active molecules. I also demonstrate a strategy to create cloud-ready pipelines for structure-based virtual screening. The major advantages of this strategy are increased productivity and high throughput. In this work, I show that Spark can be applied to virtual screening, and that it is, in general, an appropriate solution for large-scale parallel pipelining. Moreover, I illustrate how Big Data analytics are valuable in working with life sciences datasets.Secondly, I present a method to further reduce the overall time of the structured-based virtual screening strategy using machine learning and a conformal-prediction-based iterative modelling strategy. The idea is to only dock those molecules that have a better than average chance of being an inhibitor when searching for molecules that could potentially be used as drugs. Using machine learning models from this work, I built a web service to predict the target profile of multiple compounds against ready-made models for a list of targets where 3D structures are available. These target predictions can be used to understand off-target effects, for example in the early stages of drug discovery projects.Thirdly, I present a method to detect seizures in long term Electroencephalography readings - this method works in real time taking the ongoing readings in as live data streams. The method involves tackling the challenges of real-time decision-making, storing large datasets in memory and updating the prediction model with newly produced data at a rapid rate. The resulting algorithm not only classifies seizures in real time, it also learns the threshold in real time. I also present a new feature "top-k amplitude measure" for classifying which parts of the data correspond to seizures. Furthermore, this feature helps to reduce the amount of data that needs to be processed in the subsequent steps.
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| 5. |
- Akrong, Grace, et al.
(author)
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A New Pharmacokinetic-Pharmacodynamic Model To Characterize the Inoculum Effect of Acinetobacter baumannii on Polymyxin B In Vitro
- 2022
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In: Antimicrobial Agents and Chemotherapy. - : American Society for Microbiology. - 0066-4804 .- 1098-6596. ; 66:1
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Journal article (peer-reviewed)abstract
- The inoculum effect (i.e., reduction in antimicrobial activity at large starting inoculum) is a phenomenon described for various pathogens. Given that limited data exist regarding inoculum effect of Acinetobacter baumannii, we evaluated killing of A. baumannii by polymyxin B, a last-resort antibiotic, at several starting inocula and developed a pharmacokinetic-pharmacodynamic (PKPD) model to capture this phenomenon. In vitro static time-kill experiments were performed using polymyxin B at concentrations ranging from 0.125 to 128 mg/L against a clinical A. baumannii isolate at four starting inocula from 10(5) to 10(8) CFU/mL. Samples were collected up to 30 h to quantify the viable bacterial burden and were simultaneously modeled in the NONMEM software program. The expression of polymyxin B resistance genes (lpxACD, pmrCAB, and wzc), and genetic modifications were studied by RT-qPCR and DNA sequencing experiments, respectively. The PKPD model included a single homogeneous bacterial population with adaptive resistance. Polymyxin B effect was modeled as a sigmoidal E-max model and the inoculum effect as an increase of polymyxin B EC50 with increasing starting inoculum using a power function. Polymyxin B displayed a reduced activity as the starting inoculum increased: a 20-fold increase of polymyxin B EC50 was observed between the lowest and the highest inoculum. No effects of polymyxin B and inoculum size were observed on the studied genes. The proposed PKPD model successfully described and predicted the pronounced in vitro inoculum effect of A. baumannii on polymyxin B activity. These results should be further validated using other bacteria/antibiotic combinations and in vivo models.
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| 6. |
- Alvarez, Ignacio, et al.
(author)
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Proteomic and Lipidomic Profiling of Calves Experimentally Co-Infected with Influenza D Virus and Mycoplasma bovis : Insights into the Host-Pathogen Interactions
- 2024
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In: Viruses. - : MDPI. - 1999-4915. ; 16:3
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Journal article (peer-reviewed)abstract
- The role of Influenza D virus (IDV) in bovine respiratory disease remains unclear. An in vivo experiment resulted in increased clinical signs, lesions, and pathogen replication in calves co-infected with IDV and Mycoplasma bovis (M. bovis), compared to single-infected calves. The present study aimed to elucidate the host-pathogen interactions and profile the kinetics of lipid mediators in the airways of these calves. Bronchoalveolar lavage (BAL) samples collected at 2 days post-infection (dpi) were used for proteomic analyses by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Additionally, lipidomic analyses were performed by LC-MS/MS on BAL samples collected at 2, 7 and 14 dpi. Whereas M. bovis induced the expression of proteins involved in fibrin formation, IDV co-infection counteracted this coagulation mechanism and downregulated other acute-phase response proteins, such as complement component 4 (C4) and plasminogen (PLG). The reduced inflammatory response against M. bovis likely resulted in increased M. bovis replication and delayed M. bovis clearance, which led to a significantly increased abundance of oxylipids in co-infected calves. The identified induced oxylipids mainly derived from arachidonic acid; were likely oxidized by COX-1, COX-2, and LOX-5; and peaked at 7 dpi. This paper presents the first characterization of BAL proteome and lipid mediator kinetics in response to IDV and M. bovis infection in cattle and raises hypotheses regarding how IDV acts as a co-pathogen in bovine respiratory disease.
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| 7. |
- Anderlini, Michel Vincent, 1985-
(author)
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The Mundane Face of Europeanization : Norm Implementation through Expert Interactions in Georgia 2012-2020
- 2023
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Doctoral thesis (other academic/artistic)abstract
- Numerous studies, using the Europeanization theoretical framework, have looked into why and how EU-supported norms and policies are adopted in non EU-Member States, focusing either on the mechanisms through which they are diffused or on the local actors' responses to such demands. However, the practical implementation of such norms and policies in third countries has only received modest attention in academic and policy-related studies. Indeed, the “law in the books” is not necessarily the “law in action”. Going beyond the top-down approach that have extensively characterized Europeanization studies, this dissertation will operate a return to the “mundane face” of Europeanization and looks into how expert interactions matter for EU law implementation. It shows that those experts are highly enthusiast and willing to implement EU demands and adapted them to fit in their domestic context. They act as policy champions and show high degrees of policy saliency when fulfilling their tasks. Nevertheless, those champions operate in a difficult administrative and political environment that complicates EU law compliance, with low administrative capacity, high degree of staff turn-over, shortages of knowledgeable staff and political actors that might hinder EU law implementation if it is too costly or in contradiction with domestic vested interests.
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| 8. |
- Andres, Juan, et al.
(author)
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Nine questions on energy decomposition analysis
- 2019
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In: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 40:26, s. 2248-2283
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Journal article (peer-reviewed)abstract
- The paper collects the answers of the authors to the following questions: Is the lack of precision in the definition of many chemical concepts one of the reasons for the coexistence of many partition schemes? Does the adoption of a given partition scheme imply a set of more precise definitions of the underlying chemical concepts? How can one use the results of a partition scheme to improve the clarity of definitions of concepts? Are partition schemes subject to scientific Darwinism? If so, what is the influence of a community's sociological pressure in the “natural selection” process? To what extent does/can/should investigated systems influence the choice of a particular partition scheme? Do we need more focused chemical validation of Energy Decomposition Analysis (EDA) methodology and descriptors/terms in general? Is there any interest in developing common benchmarks and test sets for cross-validation of methods? Is it possible to contemplate a unified partition scheme (let us call it the “standard model” of partitioning), that is proper for all applications in chemistry, in the foreseeable future or even in principle? In the end, science is about experiments and the real world. Can one, therefore, use any experiment or experimental data be used to favor one partition scheme over another?
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| 9. |
- Audard, Vincent, et al.
(author)
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A 59-kd renal antigen as a new target for rapidly progressive glomerulonephritis
- 2007
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In: American Journal of Kidney Diseases. - : Elsevier BV. - 1523-6838 .- 0272-6386. ; 49:5, s. 710-716
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Journal article (peer-reviewed)abstract
- Anti-glomerular basement membrane (anti-GBM) antibodies are the hallmark of anti-GBM disease, which is characterized by rapidly progressive glomerulonephritis. We describe the case of a 58-year-old woman who presented with rapidly progressive glomerulonephritis with typical anti-GBM staining found by means of direct immunofluorescence microscopy, associated with linear immunoglobin G deposits on tubules. Serum analysis showed circulating anti-tubular basement membrane antibodies, but failed to detect anti-GBM antibodies. Immunoblotting showed that serum antibodies reacted with a 59-kd antigen found along both the GBM and tubular basement membrane.
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| 10. |
- Braem, Marieke G. M., et al.
(author)
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Coffee and tea consumption and the risk of ovarian cancer : a prospective cohort study and updated meta-analysis
- 2012
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In: American Journal of Clinical Nutrition. - Bethesda : American Society for Nutrition. - 0002-9165 .- 1938-3207. ; 95:5, s. 1172-1181
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Journal article (peer-reviewed)abstract
- Background: In 2007 the World Cancer Research Fund Report concluded that there was limited and inconsistent evidence for an effect of coffee and tea consumption on the risk of epithelial ovarian cancer (EOC). Objective: In the European Prospective Investigation into Cancer and Nutrition (EPIC), we aimed to investigate whether coffee intakes, tea intakes, or both are associated with the risk of EOC. Design: All women participating in the EPIC (n = 330,849) were included in this study. Data on coffee and tea consumption were collected through validated food-frequency questionnaires at baseline. HRs and 95% CIs were estimated by using Cox proportional hazards models. Furthermore, we performed an updated meta-analysis of all previous prospective studies until April 2011 by comparing the highest and lowest coffee- and tea-consumption categories as well as by using dose-response random-effects meta-regression analyses. Results: During a median follow-up of 11.7 y, 1244 women developed EOC. No association was observed between the risk of EOC and coffee consumption [HR: 1.05 (95% CI: 0.75, 1.46) for the top quintile compared with no intake] or tea consumption [HR: 1.07 (95% Cl: 0.78, 1.45) for the top quintile compared with no intake]. This lack of association between coffee and tea intake and EOC risk was confirmed by the results of our meta-analysis. Conclusion: Epidemiologic studies do not provide sufficient evidence to support an association between coffee and tea consumption and risk of ovarian cancer. Am J Clin Nutr 2012;95:1172-81.
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