| 1. |
- Bajorath, J., et al.
(author)
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Chemoinformatics and artificial intelligence colloquium: progress and challenges in developing bioactive compounds
- 2022
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In: Journal of Cheminformatics. - : Springer Science and Business Media LLC. - 1758-2946. ; 14:1
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Journal article (peer-reviewed)abstract
- We report the main conclusions of the first Chemoinformatics and Artificial Intelligence Colloquium, Mexico City, June 15–17, 2022. Fifteen lectures were presented during a virtual public event with speakers from industry, academia, and non-for-profit organizations. Twelve hundred and ninety students and academics from more than 60 countries. During the meeting, applications, challenges, and opportunities in drug discovery, de novo drug design, ADME-Tox (absorption, distribution, metabolism, excretion and toxicity) property predictions, organic chemistry, peptides, and antibiotic resistance were discussed. The program along with the recordings of all sessions are freely available at https://www.difacquim.com/english/events/2022-colloquium/.
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| 2. |
- Zhang, Shidong, et al.
(author)
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Simple and complex polymer electrolyte fuel cell stack models : A comparison
- 2018. - 13
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In: ECS Transactions. - : The Electrochemical Society. - 1938-6737 .- 1938-5862. - 9781607685395 ; 86, s. 287-300
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Conference paper (peer-reviewed)abstract
- In this paper, two distinct polymer electrolyte fuel cell stack models are constructed: a detailed numerical model (DNM) employing a fine-scale computational mesh and a coarse-mesh approach based on a distributed resistance analogy (DRA) where diffusion terms in the transport equations are replaced by rate terms. Both methods are applied to a 5-cell, high-temperature polymer electrolyte fuel cell stack with an active area of 200 cm2 per cell. The polarization curve and local current density distributions from both the DRA and DNM are compared with experimental data, finding good agreement. Temperature, pressure, Nernst potential, and species distributions are also exhibited. The DNM displays details of fine-scale local extrema not captured by the DRA; however, the latter requires orders of magnitude less computer processor power and memory for execution. Both methods provide much finer-scale results than present experimental techniques.
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| 3. |
- Andersson, M., et al.
(author)
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Coupling of lattice boltzmann and volume of fluid approaches to study the droplet behavior at the gas diffusion layer/gas channel interface
- 2018. - 13
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In: ECS Transactions. - : The Electrochemical Society. - 1938-6737 .- 1938-5862. - 9781607688600 ; 86, s. 329-336
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Conference paper (peer-reviewed)abstract
- A typical polymer electrolyte fuel cell (PEFC) flow field consists of micro/minichannels. The continues removal of liquid water from the cathode channels is a critical topic, as water droplets forming in the channels may block the transport of gaseous oxygen to the active sites, which not only gives an uneven current distribution and substantial loss of performance, but also, increases degradation rates and unstable operation. Water generated by the electrochemical reactions condenses, depending on temperature mainly, into liquid form, potentially flooding various part of the PEFC. The aim of this work is to obtain an increased understanding of the droplet behavior at the gas diffusion layer (GDL) interface with the gas channels in PEFCs by the coupling of Lattice Boltzmann (LB) and Volume of Fluid (VOF) approaches. A multiscale environment is established with input parameters in the VOF model being extracted from in-house LB calculations. It is clear that the contact angle as well as the size of the liquid droplet vary with positions at the GDL surface, depending on the stochastic GDL geometry. A VOF model describing one straight channel with one gas inlet, one liquid inlet (at the GDL surface) and one two-phase outlet is employed.
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| 4. |
- Latenstein, Anouk E. J., et al.
(author)
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Clinical Outcomes After Total Pancreatectomy A Prospective Multicenter Pan-European Snapshot Study
- 2022
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In: Annals of Surgery. - : LIPPINCOTT WILLIAMS & WILKINS. - 0003-4932 .- 1528-1140. ; 276:5, s. E536-E543
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Journal article (peer-reviewed)abstract
- Objective: To assess outcomes among patients undergoing total pancreatectomy (TP) including predictors for complications and in-hospital mortality. Background: Current studies on TP mostly originate from high-volume centers and span long time periods and therefore may not reflect daily practice. Methods: This prospective pan-European snapshot study included patients who underwent elective (primary or completion) TP in 43 centers in 16 European countries (June 2018-June 2019). Subgroup analysis included cutoff values for annual volume of pancreatoduodenectomies (<60 vs >= 60). Predictors for major complications and in-hospital mortality were assessed in multivariable logistic regression. Results: In total, 277 patients underwent TP, mostly for malignant disease (73%). Major postoperative complications occurred in 70 patients (25%). Median hospital stay was 12 days (IQR 9-18) and 40 patients were readmitted (15%). In-hospital mortality was 5% and 90-day mortality 8%. In the subgroup analysis, in-hospital mortality was lower in patients operated in centers with >= 60 pancreatoduodenectomies compared <60 (4% vs 10%, P = 0.046). In multivariable analysis, annual volume <60 pancreatoduodenectomies (OR 3.78, 95% CI 1.18-12.16, P = 0.026), age (OR 1.07, 95% CI 1.01-1.14, P = 0.046), and estimated blood loss >= 2L (OR 11.89, 95% CI 2.64-53.61, P = 0.001) were associated with in-hospital mortality. ASA >= 3 (OR 2.87, 95% CI 1.56-5.26, P = 0.001) and estimated blood loss >= 2L (OR 3.52, 95% CI 1.25-9.90, P = 0.017) were associated with major complications. Conclusion: This pan-European prospective snapshot study found a 5% inhospital mortality after TP. The identified predictors for mortality, including low-volume centers, age, and increased blood loss, may be used to improve outcomes.
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| 5. |
- Alocci, D., et al.
(author)
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GlyConnect: Glycoproteomics Goes Visual, Interactive, and Analytical
- 2019
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In: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 18:2, s. 664-677
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Journal article (peer-reviewed)abstract
- Knowledge of glycoproteins, their site-specific glycosylation patterns, and the glycan structures that they present to their recognition partners in health and disease is gradually being built on using a range of experimental approaches. The data from these analyses are increasingly being standardized and presented in various sources, from supplemental tables in publications to localized servers in investigator laboratories. Bioinformatics tools are now needed to collect these data and enable the user to search, display, and connect glycomics and glycoproteomics to other sources of related proteomics, genomics, and interactomics information. We here introduce GlyConnect (https://glyconnect.expasy.org/), the central platform of the Glycomics@ExPASy portal for glycoinformatics. GlyConnect has been developed to gather, monitor, integrate, and visualize data in a user-friendly way to facilitate the interpretation of collected glycoscience data. GlyConnect is designed to accommodate and integrate multiple data types as they are increasingly produced.
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| 6. |
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| 7. |
- Gasteiger, J., et al.
(author)
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Representative wavelengths absorption parameterization applied to satellite channels and spectral bands
- 2014
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In: Journal of Quantitative Spectroscopy and Radiative Transfer. - : Elsevier BV. - 0022-4073 .- 1879-1352. ; 148, s. 99-115
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Journal article (peer-reviewed)abstract
- Accurate modeling of wavelength-integrated radiative quantities, e.g. integrated over a spectral band or an instrument channel response function, requires computations for a large number of wavelengths if the radiation is affected by gas absorption which typically comprises a complex line structure. In order to increase computational speed of modeling radiation in the Earth׳s atmosphere, we parameterized wavelength-integrals as weighted means over representative wavelengths. We parameterized spectral bands of different widths (1 cm−1, 5 cm−1, and 15 cm−1) in the solar and thermal spectral range, as well as a number of instrument channels on the ADEOS, ALOS, EarthCARE, Envisat, ERS, Landsat, MSG, PARASOL, Proba, Sentinel, Seosat, and SPOT satellites. A root mean square relative deviation lower than 1% from a “training data set” was selected as the accuracy threshold for the parameterization of each band and channel. The training data set included high spectral resolution calculations of radiances at the top of atmosphere for a set of highly variable atmospheric states including clouds and aerosols. The gas absorption was calculated from the HITRAN 2004 spectroscopic data set and state-of-the-art continuum models using the ARTS radiative transfer model. Three representative wavelengths were required on average to fulfill the accuracy threshold. We implemented the parameterized spectral bands and satellite channels in the uvspec radiative transfer model which is part of the libRadtran software package. The parameterization data files, including the representative wavelengths and weights as well as lookup tables of absorption cross sections of various gases, are provided at the libRadtran webpage.In the paper we describe the parameterization approach and its application. We validate the approach by comparing modeling results of parameterized bands and channels with results from high spectral resolution calculations for atmospheric states that were not part of the training data set. Irradiances are not only compared at the top of atmosphere but also at the surface for which this parameterization approach was not optimized. It is found that the parameterized bands and channels provide a good compromise between computation time requirements and uncertainty for typical radiative transfer problems. In particular for satellite radiometer simulations the computation time requirement and the parameterization uncertainty is low. Band-integrated irradiances at any level as well as heating and cooling rates below 20 km can also be modeled with low uncertainty.
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| 8. |
- Kamm, C, et al.
(author)
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The fragile X tremor ataxia syndrome in the differential diagnosis of multiple system atrophy: data from the EMSA Study Group
- 2005
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In: Brain. - : Oxford University Press (OUP). - 1460-2156 .- 0006-8950. ; 128:8, s. 1855-1860
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Journal article (peer-reviewed)abstract
- The recent identification of fragile X-associated tremor ataxia syndrome (FXTAS) associated with premutations in the FMR1 gene and the possibility of clinical overlap with multiple system atrophy (MSA) has raised important questions, such as whether genetic testing for FXTAS should be performed routinely in MSA and whether positive cases might affect the specificity of current MSA diagnostic criteria. We genotyped 507 patients with clinically diagnosed or pathologically proven MSA for FMR1 repeat length. Among the 426 clinically diagnosed cases, we identified four patients carrying FMR1 premutations (0.94%). Within the subgroup of patients with probable MSA-C, three of 76 patients (3.95%) carried premutations. We identified no premutation carriers among 81 patients with pathologically proven MSA and only one carrier among 622 controls (0.16%). Our results suggest that, with proper application of current diagnostic criteria, FXTAS is very unlikely to be confused with MSA. However, slowly progressive disease or predominant tremor are useful red flags and should prompt the consideration of FXTAS. On the basis of our data, the EMSA Study Group does not recommend routine FMR1 genotyping in typical MSA patients.
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| 9. |
- Mariethoz, J., et al.
(author)
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Glycomics@ExPASy: Bridging the gap
- 2018
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In: Molecular and Cellular Proteomics. - 1535-9476. ; 17:11, s. 2164-2176
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Journal article (peer-reviewed)abstract
- Glycomics@ExPASy (https://www.expasy.org/glycomics) is the glycomics tab of ExPASy, the server of SIB Swiss Institute of Bioinformatics. It was created in 2016 to centralize web-based glycoinformatics resources developed within an international network of glycoscientists. The hosted collection currently includes mainly databases and tools created and maintained at SIB but also links to a range of reference resources popular in the glycomics community. The philosophy of our toolbox is that it should be {glycoscientist AND protein scientist}-friendly with the aim of (1) popularizing the use of bioinformatics in glycobiology and (2) emphasizing the relationship between glycobiology and protein-oriented bioinformatics resources. The scarcity of data bridging these two disciplines led us to design tools as interactive as possible based on database connectivity to facilitate data exploration and support hypothesis building. Glycomics@ExPASy was designed, and is developed, with a long-term vision in close collaboration with glycoscientists to meet as closely as possible the growing needs of the community for glycoinformatics. © 2018 Mariethoz et al.
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| 10. |
- Mueller, D., et al.
(author)
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Comparison of optical and microphysical properties of pure Saharan mineral dust observed with AERONET Sun photometer, Raman lidar, and in situ instruments during SAMUM 2006
- 2012
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In: Journal of Geophysical Research. - 0148-0227 .- 2156-2202. ; 117, s. D07211-
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Journal article (peer-reviewed)abstract
- The Saharan Mineral Dust Experiment (SAMUM) 2006, Morocco, aimed at the characterization of optical, physical, and radiative properties of Saharan dust. AERONET Sun photometer, several lidars (Raman and high-spectral-resolution instruments), and airborne and ground-based in situ instruments provided us with a comprehensive set of data on particle-shape dependent and particle-shape independent dust properties. We compare 4 measurement days in detail, and we carry out a statistical analysis for some of the inferred data products for the complete measurement period. Particle size distributions and complex refractive indices inferred from the Sun photometer observations and measured in situ aboard a research aircraft show systematic differences. We find differences in the wavelength-dependence of single-scattering albedo, compared to light-scattering computations that use data from SOAP (spectral optical absorption photometer). AERONET data products of particle size distribution, complex refractive index, and axis ratios were used to compute particle extinction-to-backscatter (lidar) ratios and linear particle depolarization ratios. We find differences for these parameters to lidar measurements of lidar ratio and particle depolarization ratio. Differences particularly exist at 355 nm, which may be the result of differences of the wavelength-dependent complex refractive index that is inferred by the methods employed in this field campaign. We discuss various error sources that may lead to the observed differences.
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