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258 results on '"Johansson B"'

1. Evaluating patient reported outcomes and experiences in a novel proton beam clinic – challenges, activities, and outcomes of the ProtonCare project

Author

Sjövall, K., Langegård, U., Fransson, Per, Nevo-Ohlsson, E., Kristensen, I., Ahlberg, K., and Johansson, B.

Subjects
Cancer nursing, Cancer och onkologi, Cancer Research, Research program planning, Radiotherapy, Oncology, Proton beam therapy, Omvårdnad, Cancer and Oncology, Genetics, Nursing, Patient reported outcomes
Abstract

Background The ProtonCare Study Group (PCSG) was formed with the purpose to develop and implement a framework for evaluation of proton beam therapy (PBT) and the related care at a novel clinic (Skandionkliniken), based on patient reported data. Method A logic model framework was used to describe the process of development and implementation of a structured plan for evaluation of PBT for all diagnoses based on patient reported data. After the mission for the project was determined, meetings with networks and stakeholders were facilitated by PCSG to identify assumptions, resources, challenges, activities, outputs, outcomes, and outcome indicators. Result This paper presents the challenges and accomplishments PCSG made so far. We describe required resources, activities, and accomplished results. The long-term outcomes that were outlined as a result of the process are two; 1) Improved knowledge about health outcomes of patients that are considered for PBT and 2) The findings will serve as a base for clinical decisions when patients are referred for PBT. Conclusion Using the logical model framework proved useful in planning and managing the ProtonCare project. As a result, the work of PCSG has so far resulted in long-lasting outcomes that creates a base for future evaluation of patients’ perspective in radiotherapy treatment in general and in PBT especially. Our experiences can be useful for other research groups facing similar challenges. Continuing research on patients´ perspective is a central part in ongoing and future research. Collaboration, cooperation, and coordination between research groups/networks from different disciplines are a significant part of the work aiming to determine the more precise role of PBT in future treatment options.

Published
2023

2. Standalone Neural ODEs with Sensitivity Analysis

Author

Jaroudi, Rym, Malý, Lukáš, Eilertsen, Gabriel, Johansson, B. Tomas, Unger, Jonas, and Baravdish, George

Subjects
FOS: Computer and information sciences, Computer Science - Machine Learning, Optimization and Control (math.OC), 68T07, 34H05, 49N45, FOS: Mathematics, Mathematics - Optimization and Control, Machine Learning (cs.LG)
Abstract

This paper presents the Standalone Neural ODE (sNODE), a continuous-depth neural ODE model capable of describing a full deep neural network. This uses a novel nonlinear conjugate gradient (NCG) descent optimization scheme for training, where the Sobolev gradient can be incorporated to improve smoothness of model weights. We also present a general formulation of the neural sensitivity problem and show how it is used in the NCG training. The sensitivity analysis provides a reliable measure of uncertainty propagation throughout a network, and can be used to study model robustness and to generate adversarial attacks. Our evaluations demonstrate that our novel formulations lead to increased robustness and performance as compared to ResNet models, and that it opens up for new opportunities for designing and developing machine learning with improved explainability., 25 pages, 15 figures; typos corrected

Published
2022

3. Learning via nonlinear conjugate gradients and depth-varying neural ODEs

Author

Baravdish, George, Eilertsen, Gabriel, Jaroudi, Rym, Johansson, B. Tomas, Mal��, Luk����, and Unger, Jonas

Subjects
FOS: Computer and information sciences, Computer Science - Machine Learning, Optimization and Control (math.OC), 68T07, 34H05, 49N45, FOS: Mathematics, Mathematics - Optimization and Control, Machine Learning (cs.LG)
Abstract

The inverse problem of supervised reconstruction of depth-variable (time-dependent) parameters in a neural ordinary differential equation (NODE) is considered, that means finding the weights of a residual network with time continuous layers. The NODE is treated as an isolated entity describing the full network as opposed to earlier research, which embedded it between pre- and post-appended layers trained by conventional methods. The proposed parameter reconstruction is done for a general first order differential equation by minimizing a cost functional covering a variety of loss functions and penalty terms. A nonlinear conjugate gradient method (NCG) is derived for the minimization. Mathematical properties are stated for the differential equation and the cost functional. The adjoint problem needed is derived together with a sensitivity problem. The sensitivity problem can estimate changes in the network output under perturbation of the trained parameters. To preserve smoothness during the iterations the Sobolev gradient is calculated and incorporated. As a proof-of-concept, numerical results are included for a NODE and two synthetic datasets, and compared with standard gradient approaches (not based on NODEs). The results show that the proposed method works well for deep learning with infinite numbers of layers, and has built-in stability and smoothness., 26 pages, 3 figures

Published
2022

4. Distractibility When Suffering from Mental Fatigue after a Mild Traumatic Brain Injury

Author

Johansson B

Subjects
medicine.medical_specialty, Physical medicine and rehabilitation, business.industry, Traumatic brain injury, Mental fatigue, education, Medicine, business, medicine.disease, behavioral disciplines and activities, humanities, psychological phenomena and processes
Abstract

Most Traumatic Brain Injuries are mild (mTBI) yet many people suffer from long-term mental fatigue and cognitive impairment. Despite comments from patients, cognitive difficulties can go undetected. Distractibility is commonly reported but is seldom included in standard neuropsychological assessment. This study was designed to investigate the effect distraction may induce in topdown and bottom-up attention among people who suffer from mental fatigue after mTBI. Thirty mTBI patients suffering from mental fatigue and 30 healthy controls performed a computerized test, including Simple Reaction Time, Choice Reaction Time and Attentional Capture tasks with a salient distractor. A slower processing speed was found in all subtests for the mTBI group and was particularly noticeable for the decision-making task. The distraction stimulus reduced processing speed for both groups, while the mTBI group made more omissions when a distractor emerged, indicating increased distractibility. However, no effect in top-down and bottom-up attention was found. Response time in the presence of a distractor was a predictor for mental fatigue, while depression and anxiety were not, showing the importance to carefully distinguish between emotional distress and mental fatigue. In conclusion, it is suggested that people suffering from mental fatigue after mTBI are slower at processing information, and this is more pronounced when a cognitive demand is added to the task. Distractibility was indicated with more omissions during distraction, but a distinction between top-down and bottom-up systems was not found. Further research is needed to better understand the link between distractibility and mental fatigue after a brain injury.

Published
2021

5. Meropenem Monotherapy is a Valid Alternative in Community Acquired Adult Acute Bacterial Meningitis (ABM)

Author

Johansson B, Lindquist L, and Fohlman J

Subjects
medicine.medical_specialty, business.industry, Internal medicine, medicine, General Medicine, business, Meropenem, Acute bacterial meningitis, medicine.drug
Abstract

Background: Meropenem (Merrem®, Meropenem®) is a broad-spectrum antibacterial carbapenem with indication for Acute Bacterial Meningitis (ABM). We wanted to specifically evaluate the effect of meropenem monotherapy, compared to standard recommended therapy. Method: A Swedish ongoing internet based quality register for ABM was started 1994 and covers the whole country with roughly 30 infectious disease clinics. After ethical approval data were extracted from the database and evaluated using conventional statistical methods (IBM SPSS Statistics 23). Results: The register contained 1708 patients altogether. All 770 patients (45%) given meropenem or cefotaxime/ampicillin were selected for this study. The age of the studied population was from 18-91 with a mean of 55 and median 60. Overall ABM mortality was 12.1% (197/1708). In the meropenem and cefotaxime/ampicillin subgroup 7.8% (60/770) died, p=0,035 and in the non-selected group 14,6 % (137/938), p

Published
2021

7. Theoretical analysis of doped graphene as cathode catalyst in Li-O2 and Na-O2 batteries -- the impact of the computational scheme

Author

Nov��i��, Katarina A., Dobrota, Ana S., Petkovi��, Milena, Johansson, B��rje, Skorodumova, Natalia V., Mentus, Slavko V., and Pa��ti, Igor A.

Subjects
Condensed Matter - Materials Science, Materials Science (cond-mat.mtrl-sci), FOS: Physical sciences
Abstract

Understanding the reactions in M-O2 cells (M = Li or Na) is of great importance for further advancement of this promising technology. Computational modelling can be helpful along this way, but an adequate approach is needed to model such complex systems. We propose a new scheme for modelling processes in M-O2 cells, where reference energies are obtained from high-level theory, CCSD(T), while the interactions of reaction intermediates with catalyst surfaces are extracted from computationally less expensive DFT. The approach is demonstrated for the case of graphene-based surfaces as model catalysts in Li-O2 and Na-O2 cells using the minimum viable mechanism. B-doped graphene was identified as the best catalyst among considered surfaces, while pristine graphene performs poorly. Moreover, we show that the inclusion of dispersion corrections for DFT has a significant impact on calculated discharge and charge potentials and suggests that long-range dispersion interactions should always be considered when graphene-based materials are modelled as electrocatalysts. Finally, we offer general guidelines for designing new ORR catalysts for M-O2 cells in terms of the optimization of the interactions of catalyst surface with reaction intermediates., 27 pages, including supplementary information, 7 figures in the main text, 1 table, 66 references, 5 figures in supplementary information

Published
2020

8. Numerical simulations in 3-dimensions of reaction–diffusion models for brain tumour growth

Author

Jaroudi, Rym, Åström, Freddie, Johansson, B. Tomas, and Baravdish, George

Abstract

We work with a well-known model of reaction–diffusion type for brain tumour growth and accomplish full 3-dimensional (3d) simulations of the tumour in time on two types of imaging data, the 3d Shepp–Logan head phantom image and an MRI T1-weighted brain scan from the Internet Brain Segmentation Repository. The source term is such that we have logistic growth. These simulations are obtained using standard finite difference approximations with novel calculations to increase speed and accuracy. Moreover, biological background to the model, its well-posedness together with a variational formulation are given. The variational formulation enable the feasibility of different derivations and modifications of the model.

Published
2020

9. Supplemental_material ��� Supplemental material for Intraoperative high dose rate brachytherapy during breast-conserving surgery: A Prospective Pilot Study

Author

Wickberg, ��., Liljegren, G., Ahlgren, J., Karlsson, L., With, A., and Johansson, B.

Subjects
FOS: Clinical medicine, 110323 Surgery
Abstract

Supplemental material, Supplemental_material for Intraoperative high dose rate brachytherapy during breast-conserving surgery: A Prospective Pilot Study by ��. Wickberg, G. Liljegren, J. Ahlgren, L. Karlsson, A. With and B. Johansson in Scandinavian Journal of Surgery

Published
2020
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10. Ischemic ECG abnormalities are associated with an increased risk for death among subjects with COPD, also among those without known heart disease

Author

Nilsson U, Blomberg A, Johansson B, Backman H, Eriksson B, and Lindberg A

Subjects
lcsh:RC705-779, ECG, Epidemiology, Ischemic heart disease, COPD, lcsh:Diseases of the respiratory system, Mortality
Abstract

Ulf Nilsson,1 Anders Blomberg,1 Bengt Johansson,1 Helena Backman,2 Berne Eriksson,3 Anne Lindberg1 1Department of Public Health and Clinical Medicine, Division of Medicine, Umeå University, Umeå, Sweden; 2Department of Public Health and Clinical Medicine, Division of Occupational and Environmental Medicine, the OLIN Unit, Umeå University, Umeå, 3Krefting Research Centre, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden Abstract presentation: An abstract, including parts of the results, has been presented at an oral session at the European Respiratory Society International Conference, London, UK, September 2016.Background: Cardiovascular comorbidity contributes to increased mortality among subjects with COPD. However, the prognostic value of ECG abnormalities in COPD has rarely been studied in population-based surveys.Aim: To assess the impact of ischemic ECG abnormalities (I-ECG) on mortality among individuals with COPD, compared to subjects with normal lung function (NLF), in a population-based study.Methods: During 2002–2004, all subjects with FEV1/VC

Published
2017

11. Construction of sundials via vectors

Author

Johansson, B. Tomas

Abstract

A method based on oblique projection is presented for construction of sundials. The derived formulas are classical, but usage of vectors and projections renders a coherent presentation rather than a number of special cases. The presented work is aimed to be useful for those taking a beginning module on vector algebra.

Published
2019

12. Risk assessment in pharmaceutical supply chains under unknown input-model parameters

Author

Akcay, Alp, Martagan, Tugce, Corlu, Canan G., Rabe, M., Juan, A.A., Mustafee, N., Skoogh, A., Jain, S., Johansson, B., and Operations Planning Acc. & Control

Subjects
ComputerApplications_COMPUTERSINOTHERSYSTEMS
Abstract

We consider a pharmaceutical supply chain where the manufacturer sources a customized product with unique attributes from a set of unreliable suppliers. We model the likelihood of a supplier to successfully deliver the product via Bayesian logistic regression and use simulation to obtain the posterior distribution of the unknown parameters of this model. We study the role of so-called input-model uncertainty in estimating the likelihood of the supply failure, which is the probability that none of the suppliers in a given supplier portfolio can successfully deliver the product. We investigate how the input-model uncertainty changes with respect to the characteristics of the historical data on the past realizations of the supplier performances and the product attributes.

Published
2019

13. On the reactivity of low coordinated atoms on foreign solid substrates as models of single atom catalysts

Author

Dobrota, A. S., Pašti, I. A., Jovanović, A. Z., Johansson, B., and Skorodumova, N. V.

Subjects
Condensed Matter - Materials Science, Materials Science (cond-mat.mtrl-sci), FOS: Physical sciences
Abstract

Catalysis has entered everyday life through a number of technological processes relying on different catalytic systems. The increasing demand for such systems requires rationalization of the use of their expensive components, like noble metal catalysts. As such, a catalyst with low noble metal concentration, in which each one of the noble atoms is active, would reach the lowest price possible. Nevertheless, there are no reactivity descriptors outlined for this type of low coordinated supported atoms. Using DFT calculations, we consider three diverse systems as models of single atom catalysts. We investigate monomers and bimetallic dimers of Ru, Rh, Pd, Ir and Pt on MgO(001), Cu adatom on thin Mo(001)-supported films (NaF, MgO and ScN) and single Pt adatoms on oxidized graphene surfaces. Reactivity of these metal atoms was probed by CO. In each case we see the interaction through the donation-backdonation mechanism. In some cases the CO adsorption energies can be linked to the position of the d-band center and the charge of the adatom. Higher positioned d-band center and less charged supported single atoms bind CO weaker. Also, in some cases metal atoms less strongly bonded to the substrate bind CO more strongly. The results suggest that the identification of common activity descriptor(s) for single metal atoms on foreign supports is a difficult task with no unique solution. However, it is also suggested that the stability of adatoms and strong anchoring to the support are prerequisites for the application of descriptor-based search for novel single atom catalysts., Comment: 19 pages, 6 figures, 66 references

Published
2019
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14. Re-enactment simulation for buffer size optimization in semiconductor back-end production

Author

Adan, Jelle, Sneijders, Stephan, Akcay, Alp, Adan, Ivo J.B.F., Rabe, M., Juan, A.A., Mustafee, N., Skoogh, A., Jain, S., Johansson, B., Operations Planning Acc. & Control, Chemical Engineering and Chemistry, and Dynamics and Control

Abstract

In this work, we propose a re-enactment simulation-based optimization method to determine the minimal total buffer capacity in an assembly line required to meet a target throughput. A distinguishing feature is the use of real-time event traces, in a fast fluid flow simulation model. Employing real-time event traces avoids the necessity to make restrictive modeling assumptions. The fluid simulation is combined with a multi start search algorithm. To demonstrate its effectiveness, the method is applied to a real-world use case in lead frame based semiconductor back-end manufacturing. This use case considers an assembly line consisting of six machines, for which the proposed method determines optimal buffer size configurations within several minutes of computational time.

Published
2018

15. The Changing Landscape for Stroke Prevention in AF: Findings From the GLORIA-AF Registry Phase 2

Author

Huisman, M. V., Rothman, K. J., Paquette, M., Teutsch, C., Diener, H. -C., Dubner, S. J., Halperin, J. L., C. S., Ma, Zint, K., Elsaesser, A., Bartels, D. B., Lip, G. Y. H., Abban, D., Abdul, N., Abelson, M., Ackermann, A., Adams, F., Adams, L., Adragao, P., Ageno, W., Aggarwal, R., Agosti, S., Marin, J. A., Aguilar, F., Aguilar Linares, J. A., Aguinaga, L., Ahmad, Z., Ainsworth, P., Al Ghalayini, K., Al Ismail, S., Alasfar, A., Alawwa, A., Al-Dallow, R., Alderson, L., Alexopoulos, D., Ali, A., Ali, M., Aliyar, P., Al-Joundi, T., Al Mahameed, S., Almassi, H., Almuti, K., Al-Obaidi, M., Alshehri, M., Altmann, U., Alves, A. R., Al-Zoebi, A., Amara, W., Amelot, M., Amjadi, N., Ammirati, F., Andrawis, N., Angoulvant, D., Annoni, G., Ansalone, G., Antonescu, S. A., Ariani, M., Arias, J. C., Armero, S., Arora, R., Arora, C., Ashcraft, W., Aslam, M. S., Astesiano, A., Audouin, P., Augenbraun, C., Aydin, S., Azar, R., Azim, A., Aziz, S., Backes, L. M., Baig, M., Bains, S., Bakbak, A., Baker, S., Bakhtiar, K., Bala, R., Banayan, J., Bandh, S., Bando, S., Banerjee, S., Bank, A., Barbarash, O., Baron, G., Barr, C., Barrera, C., Barton, J., Kes, V. B., Baula, G., Bayeh, H., Bazargani, N., Behrens, S., Bell, A., Benezet-Mazuecos, J., Benhalima, B., Berdague, P., Berg van den, B. J., Bergen van, P. F. M. M., Berngard, E., Bernstein, R., Berrospi, P., Berti, S., Bertomeu, V., Berz, A., Bettencourt, P., Betzu, R., Beyer-Westendorf, J., Bhagwat, R., Black, T., Blanco Ibaceta, J. H., Bloom, S., Blumberg, E., Bo, M., Bockisch, V., Bohmer, E., Bongiorni, M. G., Boriani, G., Bosch, R., Boswijk, D. J., Bott, J., Bottacchi, E., Kalan, M. B., Brandes, A., Bratland, B., Brautigam, D., Breton, N., Brouwers, P. J. A. M., Browne, K., Bruguera, J., Brunehaut, M., Brunschwig, C., Buathier, H., Buhl, A., Bullinga, J., Butcher, K., Cabrera Honorio, J. W., Caccavo, A., Cadinot, D., Cai, S., Calvi, V., Camm, J., Candeias, R., Capo, J., Capucci, A., Cardoso, J. N., Duarte Vera, Y. C., Carlson, B., Carvalho, P., Cary, S., Casanova, R., Casu, G., Cattan, S., Cavallini, C., Cayla, G., Cha, T. J., Cha, K. S., Chaaban, S., Chae, J. K., Challappa, K., Chand, S., Chandrashekar, H., Chang, M., Charbel, P., Chartier, L., Chatterjee, K., Cheema, A., Chen, S. -A., Chevallereau, P., Chiang, F. -T., Chiarella, F., Chih-Chan, L., Cho, Y. K., Choi, D. J., Chouinard, G., Danny, Chow, H. F., Chrysos, D., Chumakova, G., Jose Roberto Chuquiure Valenzuela, E. J., Cieza-Lara, T., Nica, V. C., Ciobotaru, V., Cislowski, D., Citerne, O., Claus, M., Clay, A., Clifford, P., Cohen, S., Cohen, A., Colivicchi, F., Collins, R., Compton, S., Connors, S., Conti, A., Buenostro, G. C., Coodley, G., Cooper, M., Corbett, L., Corey, O., Coronel, J., Corrigan, J., Cotrina Pereyra, R. Y., Cottin, Y., Coutu, B., Cracan, A., Crean, P., Crenshaw, J., Crijns, H. J. G. M., Crump, C., Cucher, F., Cudmore, D., Cui, L., Culp, J., Darius, H., Dary, P., Dascotte, O., Dauber, I., Davee, T., Davies, R., Davis, G., Davy, J. -M., Dayer, M., De La Briolle, A., de Mora, M., De Teresa, E., De Wolf, L., Decoulx, E., Deepak, S., Defaye, P., Del-Carpio Munoz, F., Brkljacic, D. D., Deluche, L., Destrac, S., Deumite, N. J., Di Legge, S., Dibon, O., Diemberger, I., Dillinger, J., Dionisio, P., Naydenov, S., Dotani, I., Dotcheva, E., D'Souza, A., Dubrey, S., Ducrocq, X., Dupljakov, D., Duthinh, V., Dutra, O. P., Dutta, D., Duvilla, N., Dy, J., Dziewas, R., Eaton, C., Eaves, W., Ebinger, M., Eck van, J. W. M., Edwards, T., Egocheaga, I., Ehrlich, C., Eisenberg, S., El Hallak, A., El Jabali, A., El Mahmoud, R., El Shahawy, M., Eldadah, Z., Elghelbazouri, F., Elhag, O., El-Hamdani, M., Elias, D., Ellery, A., El-Sayed, H., Elvan, A., Erickson, B., Espaliat, E., Essandoh, L., Everington, T., Evonich, R., Ezhov, A., Facila, L., Farsad, R., Fayard, M., Fedele, F., Gomes Ferreira, L. G., Ferreira, D., Santos, J. F., Ferrier, A., Finsen, A., First, B., Fisher, R., Floyd, J., Folk, T., Fonseca, C., Fonseca, L., Forman, S., Forsgren, M., Foster, M., Foster, N., Frais, M., Frandsen, B., Frappe, T., Freixa, R., French, W., Freydlin, M., Frickel, S., Fruntelata, A. G., Fujii, S., Fujino, Y., Fukunaga, H., Furukawa, Y., Gabelmann, M., Gabris, M., Gadsboll, N., Galin, P., Galinier, M., Ganim, R., Garcia, R., Quintana, A. G., Gartenlaub, O., Genz, C., Georger, F., Georges, J. -L., Georgeson, S., Ghanbasha, A., Giedrimas, E., Gierba, M., Gillespie, E., Giniger, A., Gkotsis, A., Gmehling, J., Gniot, J., Goethals, P., Goldberg, R., Goldmann, B., Goldscher, D., Golitsyn, S., Gomez Lopez, E. A., Gomez Mesa, J. E., Gonzalez, E., Cocina, E. G., Juanatey, C. G., Gorbunov, V., Gordon, B., Gorka, H., Gornick, C., Gorog, D., Goss, F., Gotte, A., Goube, P., Goudevenos, I., Goulden, D., Graham, B., Grande, A., Greco, C., Green, M., Greer, G., Gremmler, U., Grena, P., Grinshstein, Y., Grond, M., Gronda, E., Grondin, F., Gronefeld, G., Groot de, J. R., Guardigli, G., Guarnieri, T., Caiedo, C. G., Guignier, A., Gulizia, M., Gumbley, M., Gupta, D., Hack, T., Haerer, W., Hakas, J., Hall, C., Hampsey, J., Hananis, G., Hanbali, B., Handel, F., Hargrove, J., Hargroves, D., Harris, K., Hartley, D., Haruna, T., Hata, Y., Hayek, E., Healey, J., Hearne, S., Heggelund, G., Hemels, M. E. W., Hemery, Y., Henein, S., Henz, B., Her, S. -H., Hermany, P., Hernandes, M. E., Higashino, Y., Hill, M., Hisadome, T., Hishida, E., Hitchcock, J., Hoffer, E., Hoghton, M., Holmes, C., Hong, S. K., Houppe Nousse, M. -P., Howard, V., Hsu, L. F., Huang, C. -H., Huckins, D., Huehnergarth, K., Huizenga, A., Huntley, R., Hussein, G., Hwang, G. -S., Igbokidi, O., Iglesias, I., Ikpoh, M., Imberti, D., Ince, H., Indolfi, C., Ionova, T., Ip, J., Irles, D., Iseki, H., Ismail, Y., Israel, N., Isserman, S., Iteld, B., Ivanchura, G., Iyer, R., Iyer, V., Iza Villanueva, R. O., Jackson-Voyzey, E., Jaffrani, N., Jager, F., Jain, M., James, M., Jamon, Y., Jang, S. W., Pereira Jardim, C. A., Jarmukli, N., Jeanfreau, R., Jenkins, R., Jiang, X., Jiang, H., Jiang, T., Jiang, N., Jimenez, J., Jobe, R., Joffe, I., Johansson, B., Jones, N., Moura Jorge, J. C., Jouve, B., Jundi, M., Jung, W., Jung, B. C., Jung, K. T., Kabbani, S., Kabour, A., Kafkala, C., Kajiwara, K., Kalinina, L., Kampus, P., Kanda, J., Kapadia, S., Karim, A., Karolyi, L., Kashou, H., Kastrup, A., Katsivas, A., Kaufman, E., Kawai, K., Kawajiri, K., Kazmierski, J., Keeling, P., Kerfes, G. A., Kerr Saraiva, J. F., Ketova, G., Khaira, A., Khalid, M., Khludeeva, E., Khripun, A., Kim, D. I., Kim, D. K., Kim, N. H., Kim, K. S., Kim, Y. -H., Kim, J. B., Kim, J. S., Kinova, E., Klein, A., Kleinschnitz, C., Kmetzo, J., Kneller, G. L., Knezevic, A., Koch, S., Koenig, K., Angela Koh, S. M., Kohrmann, M., Koons, J., Korabathina, R., Korennova, O., Koschutnik, M., Kosinski, E., Kovacic, D., Kowalczyk, J., Koziolova, N., Kragten, J. A., Krause, L. U., Kreidieh, I., Krenning, B. J., Krishnaswamy, K., Krysiak, W., Kuck, K. -H., Kumar, S., Kumler, T., Kuniss, M., Kuo, J. -Y., Kuppers, A., Kurrelmeyer, K., Kwan, T., Kyo, E., Labovitz, A., Lacroix, A., Lam, A., Lanas Zanetti, F. T., Landau, C., Landini, G., Lang, W., Larsen, T. B., Laske, V., Lavandier, K., Law, N., Lee, M. H., Lee, D., Leitao, A., Lejay, D., Lelonek, M., Lenarczyk, R., Leprince, P., Lequeux, B., Leschke, M., Ley, N., Li, Z., Li, Y., Li, X., Li, W., Liang, J., Lieber, I., Lillestol, M., Limon Rodriguez, R. H., Lin, H., Lip, G., Litchfield, J., Liu, Z., Liu, X., Liu, Y., Liu, F., Liu, W., Llamas Esperon, G. A., Llisterri, J. L., Lo, T., Lo, E., Lobos, J. M., Lodde, B. -P., Loiselet, P., Lopez-Sendon, J., Lorga Filho, A. M., Lori, I., Luo, M., Lupovitch, S., Lyrer, P., Zuhairy, H. M., Ma, C., Ma, G., Ma, H., Madariaga, I., Maeno, K., Magnin, D., Mahmood, S., Mahood, K., Maid, G., Mainigi, S., Makaritsis, K., Maldonado Villalon, J. A., Malhotra, R., Malik, A., Mallecourt, C., Mallik, R., Manning, R., Manolis, A., Mantas, I., Manzur Jattin, F. G., Marcionni, N., Marin, F., Santana, A. M., Martinez, J., Martinez, L., Maskova, P., Hernandez, N. M., Matskeplishvili, S., Matsuda, K., Mavri, A., May, E., Mayer, N., Mazon, P., Mcclure, J., Mccormack, T., Mcgarity, W., Mcguire, M., Mcintyre, H., Mclaughlin, P., Mclaurin, B., Medina Palomino, F. A., Mehta, P., Mehzad, R., Meinel, A., Melandri, F., Mena, A., Meno, H., Menzies, D., Metcalf, K., Meyer, B., Miarka, J., Mibach, F., Michalski, D., Michel, P., Chreih, R. M., Mikdadi, G., Mikhail, M., Mikus, M., Milicic, D., Militaru, C., Miller, G., Milonas, C., Minescu, B., Mintale, I., Miralles, A., Mirault, T., Mistry, D., Mitchell, G., Miu, N. V., Miyamoto, N., Moccetti, T., Mohammed, A., Nor, A. M., Molina de Salazar, D. I., Molon, G., Molony, D., Mondillo, S., Mont, L., Moodley, R., Moore, R., Ribeiro Moreira, D. A., Mori, K., Moriarty, A., Morka, J., Moschos, N., Mota Gomes, M. A., Mousallem, N., Moya, A., Mugge, A., Mulhearn, T., Muller, J. -J., Muresan, C. 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Protasov, K, Prunier, L, Puleo, J, Pye, M, Qaddoura, F, Quedillac, J, Raev, D, Rahimi, S, Raisaro, A, Rama, B, Ranadive, N, Randall, K, Ranjith, N, Raposo, N, Rashid, H, Raters, C, Rauch Kroehnert, U, Rebane, T, Regner, S, Renzi, M, Reyes Rocha, M, Reza, S, Ria, L, Richter, D, Rickli, H, Rickner, K, Rieker, W, Rigo, F, Ripoll, T, Fonteles Ritt, L, Roberts, D, Pascual, C, Briones, I, Reyes, H, Roelke, M, Roman, M, Romeo, F, Ronner, E, Ronziere, T, Rooyer, F, Rosenbaum, D, Roth, S, Rozkova, N, Rubacek, M, Rubalcava, F, Rubanenko, O, Rubin, A, Borret, M, Rybak, K, Sabbour, H, Morales, O, Sakai, T, Salacata, A, Salecker, I, Salem, A, Salfity, M, Salguero, R, Salvioni, A, Samson, M, Sanchez, G, Sandesara, C, Saporito, W, Sasaoka, T, Sattar, P, Savard, D, Scala, P, Scemama, J, Schaupp, T, Schellinger, P, Scherr, C, Schmitz, K, Schmitz, B, Schmitz, L, Schnitzler, R, Schnupp, S, Schoeniger, P, Schön, N, Schuster, S, Schwimmbeck, P, Seamark, C, Seebass, R, Seidl, K, Seidman, B, Sek, J, Sekaran, L, Seko, Y, Sepulveda Varela, P, Sevilla, B, Shah, V, Shah, A, Shah, N, Shanes, J, Sharareh, A, Sharma, V, Shaw, L, Shimizu, Y, Shimomura, H, Shin, D, Shin, E, Shite, J, Shoukfeh, M, Shoultz, C, Silver, F, Sime, I, Simmers, T, Singal, D, Singh, N, Siostrzonek, P, Sirajuddin, M, Skeppholm, M, Smadja, D, Smith, R, Smith, D, Soda, H, Sofley, C, Sokal, A, Sotolongo, R, de Souza, O, Sparby, J, Spinar, J, Sprigings, D, Spyropoulos, A, Stakos, D, Steinberg, A, Steinwender, C, Stergiou, G, Stites, H, Stoikov, A, Strasser, R, Streb, W, Styliadis, I, Su, G, Su, X, Suarez, R, Sudnik, W, Sueyoshi, A, Sukles, K, Sun, L, Suneja, R, Svensson, P, Ziekenhuis, A, Szavits Nossan, J, Taggeselle, J, Takagi, Y, Takhar, A, Tallet, J, Tamm, A, Tanaka, S, Tanaka, K, Tang, A, Tang, S, Tassinari, T, Tayama, S, Tayebjee, M, Tebbe, U, Teixeira, J, Tesloianu, D, Tessier, P, The, S, Thevenin, J, Thomas, H, Timsit, S, Topkis, R, Torosoff, M, Touze, E, Traissac, T, Trendafilova, E, Troyan, B, Tsai, W, Tse, H, Tsutsui, H, Tsutsui, T, Tuininga, Y, Turakhia, M, Turk, S, Turner, W, Tveit, A, Twiddy, S, Tytus, R, Ukrainski, G, Valdovinos Chavez, S, Van De Graaff, E, Vanacker, P, Vardas, P, Vargas, M, Vassilikos, V, Vazquez, J, Venkataraman, A, Verdecchia, P, Vester, E, Vial, H, Vinereanu, D, Vlastaris, A, Vogel, C, vom Dahl, J, von Mering, M, Vora, K, Wakefield, P, Walia, J, Walter, T, Wang, M, Wang, N, Wang, F, Wang, X, Wang, Z, Wang, K, Watanabe, K, Wei, J, Weimar, C, Weinrich, R, Wen, M, Wheelan, K, Wicke, J, Wiemer, M, Wild, B, Wilke, A, Willems, S, Williams, M, Williams, D, Winkler, A, Wirtz, J, Witzenbichler, B, Wong, D, Lawrence Wong, K, Wong, B, Wozakowska Kaplon, B, Wu, Z, Wu, S, Wyatt, N, Xu, Y, Xu, X, Yamada, A, Yamamoto, K, Yamanoue, H, Yamashita, T, Bryan Yan, P, Yang, Y, Yang, T, Yao, J, Yarlagadda, C, Yeh, K, Yotov, Y, Yvorra, S, Zahn, R, Zamorano, J, Zanini, R, Zarich, S, Zebrack, J, Zenin, S, Zeuthen, E, Zhang, X, Zhang, Q, Zhang, D, Zhang, H, Zhao, S, Zhao, X, Zheng, Y, Zheng, Q, Zhou, J, Zimmermann, S, Zimmermann, R, Zukerman, L, and Zwaan van der, C

Subjects
Male, oral anticoagulation, Internationality, Middle Aged, registry, Antithrombins, Dabigatran, Stroke, Cross-Sectional Studies, Fibrinolytic Agents, Humans, Female, atrial fibrillation, Prospective Studies, Registries, Cardiology and Cardiovascular Medicine, Aged, Atrial Fibrillation
Abstract

Background GLORIA-AF (Global Registry on Long-Term Oral Antithrombotic Treatment in Patients with Atrial Fibrillation) is a prospective, global registry program describing antithrombotic treatment patterns in patients with newly diagnosed nonvalvular atrial fibrillation at risk of stroke. Phase 2 began when dabigatran, the first non–vitamin K antagonist oral anticoagulant (NOAC), became available. Objectives This study sought to describe phase 2 baseline data and compare these with the pre-NOAC era collected during phase 1. Methods During phase 2, 15,641 consenting patients were enrolled (November 2011 to December 2014); 15,092 were eligible. This pre-specified cross-sectional analysis describes eligible patients’ baseline characteristics. Atrial fibrillation disease characteristics, medical outcomes, and concomitant diseases and medications were collected. Data were analyzed using descriptive statistics. Results Of the total patients, 45.5% were female; median age was 71 (interquartile range: 64, 78) years. Patients were from Europe (47.1%), North America (22.5%), Asia (20.3%), Latin America (6.0%), and the Middle East/Africa (4.0%). Most had high stroke risk (CHA2DS2-VASc [Congestive heart failure, Hypertension, Age ≥75 years, Diabetes mellitus, previous Stroke, Vascular disease, Age 65 to 74 years, Sex category] score ≥2; 86.1%); 13.9% had moderate risk (CHA2DS2-VASc = 1). Overall, 79.9% received oral anticoagulants, of whom 47.6% received NOAC and 32.3% vitamin K antagonists (VKA); 12.1% received antiplatelet agents; 7.8% received no antithrombotic treatment. For comparison, the proportion of phase 1 patients (of N = 1,063 all eligible) prescribed VKA was 32.8%, acetylsalicylic acid 41.7%, and no therapy 20.2%. In Europe in phase 2, treatment with NOAC was more common than VKA (52.3% and 37.8%, respectively); 6.0% of patients received antiplatelet treatment; and 3.8% received no antithrombotic treatment. In North America, 52.1%, 26.2%, and 14.0% of patients received NOAC, VKA, and antiplatelet drugs, respectively; 7.5% received no antithrombotic treatment. NOAC use was less common in Asia (27.7%), where 27.5% of patients received VKA, 25.0% antiplatelet drugs, and 19.8% no antithrombotic treatment. Conclusions The baseline data from GLORIA-AF phase 2 demonstrate that in newly diagnosed nonvalvular atrial fibrillation patients, NOAC have been highly adopted into practice, becoming more frequently prescribed than VKA in Europe and North America. Worldwide, however, a large proportion of patients remain undertreated, particularly in Asia and North America. (Global Registry on Long-Term Oral Antithrombotic Treatment in Patients With Atrial Fibrillation [GLORIA-AF]; NCT01468701)

Published
2017

16. The method of fundamental solutions for problems in static thermo-elasticity with incomplete boundary data

Author

Marin, L., Karageorghis, Andreas, Lesnic, D., Johansson, B. T., and Karageorghis, Andreas [0000-0002-8399-6880]

Subjects
Inverse problems, Incomplete boundaries, 010103 numerical & computational mathematics, 01 natural sciences, Regularization parameters, Tikhonov regularization, Three dimensions, Boundary data, Method of fundamental solutions, Uniqueness, Sandwich structures, 0101 mathematics, Elasticity (economics), Thermoelasticity, Mathematics, method of fundamental solutions, Applied Mathematics, Mathematical analysis, General Engineering, Inverse problem, Boundary knot method, Singular boundary method, Elasticity, Computer Science Applications, 010101 applied mathematics, Continuous dependence, Numerical results, inverse problem, L-curve criterion, Thermo-elasticity
Abstract

An inverse problem in static thermo-elasticity is investigated. The aim is to reconstruct the unspecified boundary data, as well as the temperature and displacement inside a body from over-specified boundary data measured on an accessible portion of its boundary. The problem is linear but ill-posed. The uniqueness of the solution is established but the continuous dependence on the input data is violated. In order to reconstruct a stable and accurate solution, the method of fundamental solutions is combined with Tikhonov regularization where the regularization parameter is selected based on the L-curve criterion. Numerical results are presented in both two and three dimensions showing the feasibility and ease of implementation of the proposed technique. © 2016 Informa UK Limited, trading as Taylor & Francis Group. 25 5 652 673

Published
2016

17. WHEN IT GOES IT ALL GOES? LONGITUDINAL WITHIN-PERSON RELATIONS BETWEEN COGNITIVE AND PHYSICAL FUNCTION IN OLD AGE

Author

Stenling, A, Praetorius Björk, M, Johansson, B, and Lindwall, M

Subjects
Abstracts
Abstract

Previous studies suggest a relation between cognitive and physical function in later life that is influenced by a shared common cause. However, most previous studies have used between-person approaches and few have examined the directionality of the relations between cognitive and physical function. In the present study, we examined directional within-person relations between cognitive and physical function in old age. Data were drawn from the OCTO Twin Study; a Swedish population-based sample including twins aged 80 years and older. We included 468 participants in the analyses (individuals with dementia were excluded). Four cognitive tests (episodic memory, processing speed, semantic knowledge, spatial ability) and two measures of physical function (grip strength, pulmonary function) were used and participants were examined five times at two-year intervals. Longitudinal within-person relations between cognitive and physical function were examined using latent curve models with structured residuals. There was a positive reciprocal within-person relation between grip strength and semantic knowledge; no other relations involving grip strength were statistically significant. Positive reciprocal relations were found between pulmonary function and processing speed, semantic knowledge, and spatial ability. Pulmonary function positively predicted episodic memory, but not vice versa. The reciprocal relations support the hypothesis of a shared common cause for pulmonary and cognitive function, but not for grip strength and cognitive function. The high oxygen demand of the brain may explain why lung function affects cognitive function, whereas neuroselection (i.e., people with better cognitive function choose healthier lives) may explain why cognitive function affects lung function.

Published
2018

18. COGNITIVE RESERVE ACROSS THE LIFE COURSE, APOE, AND LATE LIFE COGNITIVE TRAJECTORIES

Author

Praetorius Björk, M, Engelbrekt Rolstad, S, and Johansson, B

Subjects
Abstracts
Abstract

Few studies have examined the associations among cognitive reserve (CR), APOE, and late life cognition. In the present study we examined measures of CR across the lifespan (i.e. early life- midlife- and late life) in relation to level of cognitive performance and change in late life. We also examined whether and how these relationships are affected by different time metrics by comparing the effects of chronological age with time to death. The analyses were conducted in a sample of 501 initially non-demented individuals, aged 80 years and older, followed until death. Cognition was measured using the MMSE-test (Mini-Mental State Examination). The results indicate that the CR measures were related to level of performance as well as change in MMSE. Yet, CR at different stages of life influenced cognition variously depending on use of the age- or death-related model. In the age-based model, late life cognitive activity was related to level of MMSE while early life CR was associated with a terminal decline trajectory. Associations among late life cognitive functioning, cognitive reserve and APOE status were, however, mixed and less conclusive.

Published
2018

19. An iterative regularizing method for an incomplete boundary data problem for the biharmonic equation

Author

Chapko, Roman and Johansson, B. Tomas

Abstract

An incomplete boundary data problem for the biharmonic equation is considered, where the displacement is known throughout the boundary of the solution domain whilst the normal derivative and bending moment are specified on only a portion of the boundary. For this inverse ill‐posed problem an iterative regularizing method is proposed for the stable data reconstruction on the underspecified boundary part. Convergence is proven by showing that the method can be written as a Landweber‐type procedure for an operator formulation of the incomplete data problem. This reformulation renders a stopping rule, the discrepancy principle, for terminating the iterations in the case of noisy data. Uniqueness of a solution to the considered problem is also shown.

Published
2018

20. A boundary integral equation method for numerical solution of parabolic and hyperbolic Cauchy problems

Author

Chapko, Roman and Johansson, B. Tomas

Abstract

We present a unified boundary integral approach for the stable numerical solution of the ill-posed Cauchy problem for the heat and wave equation. The method is based on a transformation in time (semi-discretisation) using either the method of Rothe or the Laguerre transform, to generate a Cauchy problem for a sequence of inhomogenous elliptic equations; the total entity of sequences is termed an elliptic system. For this stationary system, following a recent integral approach for the Cauchy problem for the Laplace equation, the solution is represented as a sequence of single-layer potentials invoking what is known as a fundamental sequence of the elliptic system thereby avoiding the use of volume potentials and domain discretisation. Matching the given data, a system of boundary integral equations is obtained for finding a sequence of layer densities. Full discretisation is obtained via a Nyström method together with the use of Tikhonov regularization for the obtained linear systems. Numerical results are included both for the heat and wave equation confirming the practical usefulness, in terms of accuracy and resourceful use of computational effort, of the proposed approach.

Published
2018

21. An elementary algorithm to evaluate trigonometric functions to high precision

Author

Johansson, B. Tomas

Subjects
Computer Science::Hardware Architecture, Hardware_ARITHMETICANDLOGICSTRUCTURES
Abstract

Evaluation of the cosine function is done via a simple Cordic-like algorithm, together with a package for handling arbitrary-precision arithmetic in the computer program Matlab. Approximations to the cosine function having hundreds of correct decimals are presented with a discussion around errors and implementation.

Published
2018

22. Simulation-based assessment of the stationary tail distribution of a stochastic differential equation

Author

Bisewski, K., Crommelin, D., Mandjes, M., Rabe, M., Juan, A.A., Mustafee, N., Skoogh, A., Jain, S., Johansson, B., Stochastics (KDV, FNWI), and Analysis (KDV, FNWI)

Abstract

A commonly used approach to analyzing stochastic differential equations (SDEs) relies on performing Monte Carlo simulation with a discrete-time counterpart. In this paper we study the impact of such a time-discretization when assessing the stationary tail distribution. For a family of semi-implicit Euler discretization schemes with time-step h > 0, we quantify the relative error due to the discretization, as a function of h and the exceedance level x. By studying the existence of certain (polynomial and exponential) moments, using a sequence of prototypical examples, we demonstrate that this error may tend to 0 or ∞. The results show that the original shape of the tail can be heavily affected by the discretization. The cases studied indicate that one has to be very careful when estimating the stationary tail distribution using Euler discretization schemes.

Published
2018

23. Simulation in Facilitation of Operations Management Education

Author

van der Zee, D.J., Sloot, S., Rabe, M., Mustafee, N., Skoogh, A., Jain, S., Johansson, B., SOM OPERA, and Value, Affordability and Sustainability (VALUE)

Abstract

Traditionally, discrete event simulation is associated with logistic system analysis due to its role as an operations research method. In this article, we consider a multiple case study on the alternative use of simulation for operations management education. When stressing the role of the student or trainee instead of operations—as in operations research—alternative demands on model set up and use arise. Identifying such demands and ways to deal with them extends simulation methodology by showing how to exploit existing simulation knowledge and tools for pedagogic purposes. Our multiple case study evaluates four simulation-based games reflecting operations systems in health care and manufacturing. Respective games target learning activities of a different nature. Outcomes of the evaluation provide insights on modelling requirements, and guidelines and good practices that are supportive in meeting these.

Published
2018

24. Panel: Education on Simulation Model Simplification - Beyond the Rules of Thumb

Author

van der Zee, D.J., Tako, A. A., Fishwick, P., Robinson, S., Rose, O., Rabe, M., Juan, A.A., Mustafee, N., Skoogh, A., Jain, S., Johansson, B., SOM OPERA, and Value, Affordability and Sustainability (VALUE)

Abstract

Most management problems addressed by simulation studies can be characterized as complex and difficult to analyze. Simplification is instrumental in creating and employing simulation models that are useful – by focusing on those system elements that matter, and feasible – by reducing study efforts. Although simplification is considered a fundamental modelling activity, simulation educational support for mastering associated modelling skills is limited. Main textbooks either do not address this topic or tend to restrict their guidance to a few rules of thumb. This reflects how the topic of simulation model simplification is underdeveloped, despite the field of simulation being around 50 years of age. The purpose of this panel is to initiate a discussion about the way we teach simulation model simplification with the view to identifying improvements. This paper addresses the motivation for the panel, and presents panelists’ “positions” about the way forward for education on simulation model simplification.

Published
2018

25. Properties of a method of fundamental solutions for the parabolic heat equation

Author

Johansson, B. Tomas

Abstract

We show that a set of fundamental solutions to the parabolic heat equation, with each element in the set corresponding to a point source located on a given surface with the number of source points being dense on this surface, constitute a linearly independent and dense set with respect to the standard inner product of square integrable functions, both on lateral- and time-boundaries. This result leads naturally to a method of numerically approximating solutions to the parabolic heat equation denoted a method of fundamental solutions (MFS). A discussion around convergence of such an approximation is included.

Published
2017

26. Challenges for critical infrastructure resilience : cascading effects of payment system disruptions

Author

Laere, J., Berggren, P., Per Gustavsson, Ibrahim, O., Johansson, B., Larsson, A., Lindqwister, T., Olsson, L., and Wiberg, C.

Subjects
Critical infrastructures, payment system, resilience, Other Computer and Information Science, Systemvetenskap, informationssystem och informatik, collective resilience, Annan data- och informationsvetenskap, Information Systems
Abstract

Critical infrastructures become more and more entangled and rely extensively on information technology. A deeper insight into the relationships between critical infrastructures enables the actors involved to more quickly understand the severity of information technology disruptions and to identify robust cross-functional mitigating actions. This study illustrates how and why disruptions in the payment system in Sweden could create cascading effects in other critical infrastructures with potentially severe consequences for many citizens, government institutions and companies. Data from document studies, interviews and workshops with field experts reveal seven challenges for collective cross-functional critical infrastructure resilience that need to be dealt with: 1) Shortage of food, fuel, cash, medicine; 2) Limited capacity of alternative payment solutions; 3) Cities are more vulnerable than the countryside; 4) Economically vulnerable groups in society are more severely affected; 5) Trust maintenance needs; 6) Crisis communication needs; 7) Fragmentation of responsibility for critical infrastructures across many actors.

Published
2017

27. Work-related stress assessed by a text message single-item stress question

Author

Arapovic-Johansson, B., Wåhlin, Charlotte, Kwak, L., Björklund, C., and Jensen, I.

Subjects
Arbetsmedicin och miljömedicin, Occupational Health and Environmental Health, Predictive validity, screening, single-item question, text message, work-related stress
Abstract

Background Given the prevalence of work stress-related ill-health in the Western world, it is important to find cost-effective, easy-to-use and valid measures which can be used both in research and in practice. Aims To examine the validity and reliability of the single-item stress question (SISQ), distributed weekly by short message service (SMS) and used for measurement of work-related stress. Methods The convergent validity was assessed through associations between the SISQ and subscales of the Job Demand-Control-Support model, the Effort-Reward Imbalance model and scales measuring depression, exhaustion and sleep. The predictive validity was assessed using SISQ data collected through SMS. The reliability was analysed by the test-retest procedure. Results Correlations between the SISQ and all the subscales except for job strain and esteem reward were significant, ranging from -0.186 to 0.627. The SISQ could also predict sick leave, depression and exhaustion at 12-month follow-up. The analysis on reliability revealed a satisfactory stability with a weighted kappa between 0.804 and 0.868. Conclusions The SISQ, administered through SMS, can be used for the screening of stress levels in a working population.

Published
2017

28. Assessment of Patterns of Patient-Reported Outcomes in Adults with Congenital Heart disease - International Study (APPROACH-IS): rationale, design, and methods

Author

Apers S, Kovacs AH, Luyckx K, Alday L, Berghammer M, Budts W, Callus E, Caruana M, Chidambarathanu S, Cook SC, Dellborg M, Enomoto J, Eriksen K, Fernandes SM, Jackson JL, Johansson B, Khairy P, Kutty S, Menahem S, Rempel G, Sluman MA, Soufi A, Thomet C, Veldtman G, Wang JK, White K, Moons P, APPROACH-IS consortium, International Society for Adult Congenital Heart Disease (ISACHD). Alday L, Maisuls H, Cabrera M, Eaton S, Larion R, FengWang Q, Van Deyk K, Goossens E, Rassart J, Mackie A, Ballantyne R, Rankin K, Norris C, Taylor D, Vondermuhll I, Windram J, Heggie P, Lasiuk G, Proietti A, Dore A, Mercier LA, Mongeon FP, Marcotte F, Ibrahim R, Mondésert B, Côté MC, Kovacs A, Oechslin E, Bandyopadhyay M, Di Filippo S, Sassolas F, Bozio A, Farzana F, Lakshmi N, Quadri E, Chessa M, Campioni G, Giamberti A, Mizuno Y, Grech V, Vella S, Mifsud A, Borg N, Chircop D, Balbi MM, Critien RV, Farrugia J, Gatt Y, Muscat D, Estensen ME, Mattson E, Strandberg A, Karlström-Hallberg P, Kronhamn AK, Schwerzman M, Huber M, Lu CW, Yang HL, Hua YC, Mulder B, Sluman M, Post M, Pieper E, Peels K, Waskowsky M, Faust M, Lozier C, Reed C, Hilfer J, Daniels C, Jackson J, Chamberlain C, Cook S, Hindes M, Cedars A, Jewish B, Rompfh A, Fernandes S, MacMillen K., Apers, S, Kovacs, Ah, Luyckx, K, Alday, L, Berghammer, M, Budts, W, Callus, E, Caruana, M, Chidambarathanu, S, Cook, Sc, Dellborg, M, Enomoto, J, Eriksen, K, Fernandes, Sm, Jackson, Jl, Johansson, B, Khairy, P, Kutty, S, Menahem, S, Rempel, G, Sluman, Ma, Soufi, A, Thomet, C, Veldtman, G, Wang, Jk, White, K, Moons, P, APPROACH-IS, Consortium, International Society for Adult Congenital Heart Disease (ISACHD)., Alday L, Maisuls, H, Cabrera, M, Eaton, S, Larion, R, Fengwang, Q, Van Deyk, K, Goossens, E, Rassart, J, Mackie, A, Ballantyne, R, Rankin, K, Norris, C, Taylor, D, Vondermuhll, I, Windram, J, Heggie, P, Lasiuk, G, Proietti, A, Dore, A, Mercier, La, Mongeon, Fp, Marcotte, F, Ibrahim, R, Mondésert, B, Côté, Mc, Kovacs, A, Oechslin, E, Bandyopadhyay, M, Di Filippo, S, Sassolas, F, Bozio, A, Farzana, F, Lakshmi, N, Quadri, E, Chessa, M, Campioni, G, Giamberti, A, Mizuno, Y, Grech, V, Vella, S, Mifsud, A, Borg, N, Chircop, D, Balbi, Mm, Critien, Rv, Farrugia, J, Gatt, Y, Muscat, D, Estensen, Me, Mattson, E, Strandberg, A, Karlström-Hallberg, P, Kronhamn, Ak, Schwerzman, M, Huber, M, Lu, Cw, Yang, Hl, Hua, Yc, Mulder, B, Sluman, M, Post, M, Pieper, E, Peels, K, Waskowsky, M, Faust, M, Lozier, C, Reed, C, Hilfer, J, Daniels, C, Jackson, J, Chamberlain, C, Cook, S, Hindes, M, Cedars, A, Jewish, B, Rompfh, A, Fernandes, S, and Macmillen, K.

Published
2015

29. Analyzing of in-cylinder flow structures and cyclic variations of partially premixed combustion in a light duty engine

Author

Tanov, S., Johansson, B, Izadi Najafabadi, M., Wang, H., and Power & Flow

Subjects
Physics::Fluid Dynamics, High-speed particle image velocimetry, Partially premixed combustion, Cycle to cycle variation, Physics::Chemical Physics, Proper orthogonal decomposition, Multiple injection strategies
Abstract

Partially Premixed Combustion (PPC) strategy offers the potential for simultaneously reduction of NOx and soot emissions with high efficiency. This low temperature combustion strategy involves a proper mixing of fuel and air prior to auto-ignition. During ignition delay (ID) the exact amount of premixing is crucial for the combustion behaviour and emission formation. In this article, high-speed particle image velocimetry (HS-PIV) has been applied to characterise the in-cylinder flow and cycle-to-cycle variations in a light-duty optical engine during fired conditions. The engine is operated at 800 rpm and at a constant CA 50 (~ 8 CAD aTDC). Multiple injections strategies (single, double and triple injections) have been applied to investigate their influence on the flow inside the piston bowl and squish region. The 2D velocity fields are evaluated and investigated over a range of crank angles in the compression and expansion strokes in order to understand the cycle-to-cycle variations. To investigate the problem of cyclic- variations on in-cylinder flows the phase-invariant proper orthogonal decomposition (POD) technique was used. The POD decomposition technique provides a classification method based on an energy criterion by which the mean flow is seen as a superposition of coherent structures. From their temporal coefficients it is possible to characterize its dynamical behaviour.

Published
2016

30. Time-resolved in-cylinder PIV measurement in a light duty optical engine under PPC conditions

Author

Wang, H., Tanov, S., Izadi Najafabadi, M., Wang, Z., Johansson, B., and Power & Flow

Abstract

The understanding of in-cylinder flow field is one of the keys to realize Partially Premixed Combustion (PPC) for internal combustion engines, which has potential to achieve high combustion efficiency with low soot and NOx emissions. In this work, time resolved Particle Image Velocimetry (PIV) was performed to measure the flow field inside the cylinder of a single-cylinder light-duty optical diesel engine. The engine was modified to Bowditch configuration, and was installed with a quartz piston and a transparent cylinder liner, to allow optical access. The geometry of the quartz piston crown is based on the regular combustion chamber design of mass produced diesel engine, including a re-entrant bowl shape. This causes severe distortion on the obtained images, which has to be handled by a distortion correction method before PIV process. The in-cylinder flow structures in a vertical plane at the center of cylinder were obtained both within the piston bowl and within the squish volume, during the compression and expansion stroke. Measurements were performed under three different injection strategies as well as motored engine condition. Both the instantaneous flow field from single cycle and ensemble average flow field calculated from 100 cycles at motored engine condition show a well match with previous studies. The results from fired engine conditions show different Interaction between injected fuel and in-cylinder air at different Crank Angle Degrees (CADs) with different injection strategies. All the results in this study can provide a quantitative dataset being useful to model validation of numerical simulation work to investigate PPC engine more.

Published
2016

31. Fuel and combustion stratification study of Partially Premixed Combustion

Author

Izadi Najafabadi, M., Dam, N., Somers, B., Johansson, B., Power & Flow, Group Deen, and Group Somers

Abstract

Relatively high levels of stratification is one of the main advantages of Partially Premixed Combustion (PPC) over the Homogeneous Charge Compression Ignition (HCCI) concept. Fuel stratification smoothens heat release and improves controllability of this kind of combustion. However, the lack of a clear definition of “fuel and combustion stratifications” is obvious in literature. Hence, it is difficult to compare stratification levels of different PPC strategies or other combustion concepts. The main objective of this study is to define the fuel and combustion stratifications based on the fuel tracer LIF and OH* chemiluminescence images, respectively. A light duty optical engine has been used to perform the measurements. Four experimental points are evaluated, with injection timings in both the homogeneous and the stratified regimes. Twodimensional Fourier transforms of fuel distribution and chemiluminescence images provide the range of spatial frequencies in these images. This method gives the opportunity to separate a specific range of frequencies related to fuel and combustion stratification. The signal energy content in this range is used to define the stratification, using an appropriate normalization procedure. The results indicate that this new definition is a promising method to compare the level of stratification between different experiments.

Published
2016

32. Transmission of HIV drug resistance and the predicted effect on current first-line regimens in Europe

Author

Hofstra, L.M. Sauvageot, N. Albert, J. Alexiev, I. Garcia, F. Struck, D. Van De Vijver, D.A.M.C. Åsjö, B. Beshkov, D. Coughlan, S. Descamps, D. Griskevicius, A. Hamouda, O. Horban, A. Van Kasteren, M. Kolupajeva, T. Kostrikis, L.G. Liitsola, K. Linka, M. Mor, O. Nielsen, C. Otelea, D. Paraskevis, D. Paredes, R. Poljak, M. Puchhammer-Stöckl, E. Sönnerborg, A. Staneková, D. Stanojevic, M. Van Laethem, K. Zazzi, M. Lepej, S.Z. Boucher, C.A.B. Schmit, J.-C. Wensing, A.M.J. Puchhammer-Stockl, E. Sarcletti, M. Schmied, B. Geit, M. Balluch, G. Vandamme, A.-M. Vercauteren, J. Derdelinckx, I. Sasse, A. Bogaert, M. Ceunen, H. De Roo, A. De Wit, S. Echahidi, F. Fransen, K. Goffard, J.-C. Goubau, P. Goudeseune, E. Yombi, J.-C. Lacor, P. Liesnard, C. Moutschen, M. Pierard, D. Rens, R. Schrooten, Y. Vaira, D. Vandekerckhove, L.P.R. Van Den Heuvel, A. Van Der Gucht, B. Van Ranst, M. Van Wijngaerden, E. Vandercam, B. Vekemans, M. Verhofstede, C. Clumeck, N. Begovac, J. Demetriades, I. Kousiappa, I. Demetriou, V. Hezka, J. Maly, M. Machala, L. Jørgensen, L.B. Gerstoft, J. Mathiesen, L. Pedersen, C. Nielsen, H. Laursen, A. Kvinesdal, B. Ristola, M. Suni, J. Sutinen, J. Assoumou, L. Castor, G. Grude, M. Flandre, P. Storto, A. Kücherer, C. Berg, T. Braun, P. Poggensee, G. Däumer, M. Eberle, J. Heiken, H. Kaiser, R. Knechten, H. Korn, K. Müller, H. Neifer, S. Schmidt, B. Walter, H. Gunsenheimer-Bartmeyer, B. Harrer, T. Hatzakis, A. Zavitsanou, A. Vassilakis, A. Lazanas, M. Chini, M. Lioni, A. Sakka, V. Kourkounti, S. Paparizos, V. Antoniadou, A. Papadopoulos, A. Poulakou, G. Katsarolis, I. Protopapas, K. Chryssos, G. Drimis, S. Gargalianos, P. Xylomenos, G. Lourida, G. Psichogiou, M. Daikos, G.L. Sipsas, N.V. Kontos, A. Gamaletsou, M.N. Koratzanis, G. Sambatakou, E. Mariolis, H. Skoutelis, A. Papastamopoulos, V. Georgiou, O. Panagopoulos, P. Maltezos, E. De Gascun, C. Byrne, C. Duffy, M. Bergin, C. Reidy, D. Farrell, G. Lambert, J. O'Connor, E. Rochford, A. Low, J. Coakely, P. O'Dea, S. Hall, W. Levi, I. Chemtob, D. Grossman, Z. De Luca, A. Balotta, C. Riva, C. Mussini, C. Caramma, I. Capetti, A. Colombo, M.C. Rossi, C. Prati, F. Tramuto, F. Vitale, F. Ciccozzi, M. Angarano, G. Rezza, G. Vasins, O. Lipnickiene, V. Hemmer, R. Arendt, V. Michaux, C. Staub, T. Sequin-Devaux, C. Van Kessel, A. Van Bentum, P.H.M. Brinkman, K. Connell, B.J. Van Der Ende, M.E. Hoepelman, I.M. Kuipers, M. Langebeek, N. Richter, C. Santegoets, R.M.W.J. Schrijnders-Gudde, L. Schuurman, R. Van De Ven, B.J.M. Kran, A.-M.B. Ormaasen, V. Aavitsland, P. Stanczak, J.J. Stanczak, G.P. Firlag-Burkacka, E. Wiercinska-Drapalo, A. Jablonowska, E. Maolepsza, E. Leszczyszyn-Pynka, M. Szata, W. Camacho, R. Palma, C. Borges, F. Paixão, T. Duque, V. Araújo, F. Paraschiv, S. Tudor, A.M. Cernat, R. Chiriac, C. Dumitrescu, F. Prisecariu, L.J. Jevtovic, Dj. Salemovic, D. Stanekova, D. Habekova, M. Chabadová, Z. Drobkova, T. Bukovinova, P. Shunnar, A. Truska, P. Lunar, M. Babic, D. Tomazic, J. Vidmar, L. Vovko, T. Karner, P. Monge, S. Moreno, S. Del Amo, J. Asensi, V. Sirvent, J.L. De Mendoza, C. Delgado, R. Gutiérrez, F. Berenguer, J. Garcia-Bujalance, S. Stella, N. De Los Santos, I. Blanco, J.R. Dalmau, D. Rivero, M. Segura, F. Elías, M.J.P. Alvarez, M. Chueca, N. Rodríguez-Martín, C. Vidal, C. Palomares, J.C. Viciana, I. Viciana, P. Cordoba, J. Aguilera, A. Domingo, P. Galindo, M.J. Miralles, C. Del Pozo, M.A. Ribera, E. Iribarren, J.A. Ruiz, L. De La Torre, J. Vidal, F. Clotet, B. Heidarian, A. Aperia-Peipke, K. Axelsson, M. Mild, M. Karlsson, A. Thalme, A. Navér, L. Bratt, G. Blaxhult, A. Gisslén, M. Svennerholm, B. Björkman, P. Säll, C. Mellgren, Å. Lindholm, A. Kuylenstierna, N. Montelius, R. Azimi, F. Johansson, B. Carlsson, M. Johansson, E. Ljungberg, B. Ekvall, H. Strand, A. Mäkitalo, S. Öberg, S. Holmblad, P. Höfer, M. Holmberg, H. Josefson, P. Ryding, U. Bergbrant, I. SPREAD Program

Abstract

Background. Numerous studies have shown that baseline drug resistance patterns may influence the outcome of antiretroviral therapy. Therefore, guidelines recommend drug resistance testing to guide the choice of initial regimen. In addition to optimizing individual patient management, these baseline resistance data enable transmitted drug resistance (TDR) to be surveyed for public health purposes. The SPREAD program systematically collects data to gain insight into TDR occurring in Europe since 2001. Methods. Demographic, clinical, and virological data from 4140 antiretroviral-naive human immunodeficiency virus (HIV)-infected individuals from 26 countries who were newly diagnosed between 2008 and 2010 were analyzed. Evidence of TDR was defined using the WHO list for surveillance of drug resistance mutations. Prevalence of TDR was assessed over time by comparing the results to SPREAD data from 2002 to 2007. Baseline susceptibility to antiretroviral drugs was predicted using the Stanford HIVdb program version 7.0. Results. The overall prevalence of TDR did not change significantly over time and was 8.3% (95% confidence interval, 7.2%-9.5%) in 2008-2010. The most frequent indicators of TDR were nucleoside reverse transcriptase inhibitor (NRTI) mutations (4.5%), followed by nonnucleoside reverse transcriptase inhibitor (NNRTI) mutations (2.9%) and protease inhibitor mutations (2.0%). Baseline mutations were most predictive of reduced susceptibility to initial NNRTI-based regimens: 4.5% and 6.5% of patient isolates were predicted to have resistance to regimens containing efavirenz or rilpivirine, respectively, independent of current NRTI backbones. Conclusions. Although TDR was highest for NRTIs, the impact of baseline drug resistance patterns on susceptibility was largest for NNRTIs. The prevalence of TDR assessed by epidemiological surveys does not clearly indicate to what degree susceptibility to different drug classes is affected. © The Author 2015.

Published
2016

33. Transmission of HIV Drug Resistance and the Predicted Effect on Current First-line Regimens in Europe

Author

Moutschen, M., Hofstra, Laura Marije Arije, Sauvageot, Nicolas, Albert, Jan, Alexiev, Ivailo, Garcia, Federico, Struck, Daniel, Van, de Vijver, Åsjö, Birgitta, Beshkov, Danail, Coughlan, Suzie, Descamps, Diane, Griskevicius, Algirdas, Hamouda, Osamah, Horban, Andrzej, Van Kasteren, Marjo, Kolupajeva, Tatjana, Kostrikis, Leontios G., Liitsola, Kirsi, Linka, Marek, Mor, Orna, Nielsen, Claus, Otelea, Dan, Paraskevis, Dimitrios N., Paredes, Roger, Poljak, Mario, Puchhammer-Stöckl, Elisabeth, Sönnerborg, Anders, Staneková, Danica, Stanojevic, Maja, Van Laethem, Kristel, Zazzi, Maurizio, Zidovec Lepej, Snjezana, Boucher, Charles A. B., Schmit, Jean-Claude, Wensing, Annemarie M. J., Puchhammer-Stockl, E., Sarcletti, M., Schmied, B., Geit, M., Balluch, G., Vandamme, A. M., Vercauteren, J., Derdelinckx, I., Sasse, A., Bogaert, M., Ceunen, H., De Roo, A., De Wit, S., Echahidi, F., Fransen, K., Goffard, J. -C, Goubau, P., Goudeseune, E., Yombi, J. -C, Lacor, P., Liesnard, C., Pierard, D., Rens, R., Schrooten, Y., Vaira, D., Vandekerckhove, L. P. R., Van, den Heuvel, Van, Der Gucht, Van Ranst, M., Van Wijngaerden, E., Vandercam, B., Vekemans, M., Verhofstede, C., Clumeck, N., Van Laethem, K., Lepej, S. Z., Begovac, J., Demetriades, Ioannis, Kousiappa, Ioanna, Demetriou, Victoria L., Hezka, Johana, Linka, M., Maly, M., Machala, L., Nielsen, C., Jørgensen, L. B., Gerstoft, J., Mathiesen, L., Pedersen, C., Nielsen, H., Laursen, A., Kvinesdal, B., Liitsola, K., Ristola, M., Suni, J., Sutinen, J., Descamps, D., Assoumou, L., Castor, G., Grude, M., Flandre, P., Storto, A., Hamouda, O., Kücherer, C., Berg, T., Braun, P., Poggensee, G., Däumer, M., Eberle, J., Heiken, H., Kaiser, R., Knechten, H., Korn, K., Müller, H., Neifer, S., Schmidt, B., Walter, H., Gunsenheimer-Bartmeyer, B., Harrer, T., Hatzakis, Angelos E., Zavitsanou, Assimina, Vassilakis, A., Lazanas, Marios C., Chini, Maria C., Lioni, A., Sakka, V., Kourkounti, Sofia, Paparizos, Vassilios A., Antoniadou, Anastasia C., Papadopoulos, Antonios I., Poulakou, Garyphallia G., Katsarolis, I., Protopapas, K., Chryssos, Georgios, Drimis, Stylianos, Gargalianos, Panagiotis, Xylomenos, Georgios, Lourida, G., Psichogiou, Mina A., Daikos, George L., Sipsas, N. V., Kontos, Athanasios N., Gamaletsou, M. N., Koratzanis, Georgios, Sambatakou, H., Mariolis, H., Skoutelis, A., Papastamopoulos, V., Georgiou, O., Panagopoulos, Periklis, Maltezos, E., Coughlan, S., De Gascun, C., Byrne, C., Duffy, M., Bergin, C., Reidy, D., Farrell, G., Lambert, J., O'Connor, E., Rochford, A., Low, J., Coakely, P., O'Dea, S., Hall, W., Mor, O., Levi, I., Chemtob, D., Grossman, Z., Zazzi, M., de Luca, A., Balotta, Claudia, Riva, C., Mussini, C., Caramma, I., Capetti, A., Colombo, M. C., Rossi, C., Prati, F., Tramuto, F., Vitale, F., Ciccozzi, M., Angarano, G., Rezza, G., Kolupajeva, T., Vasins, O., Griskevicius, A., Lipnickiene, V., Schmit, J. C., Struck, D., Hemmer, R., Arendt, V., Michaux, C., Staub, T., Sequin-Devaux, C., Wensing, A. M. J., Boucher, C. A. B., van, de Vijver, van Kessel, A., van Bentum, P. H. M., Brinkman, K., Connell, B. J., van, der Ende, Hoepelman, I. M., van Kasteren, M., Kuipers, M., Langebeek, N., Richter, C., Santegoets, R. M. W. J., Schrijnders-Gudde, L., Schuurman, R., van, de Ven, Kran, A. -M B., Ormaasen, V., Aavitsland, P., Horban, A., Stanczak, J. J., Stanczak, G. P., Firlag-Burkacka, E., Wiercinska-Drapalo, A., Jablonowska, E., Maolepsza, E., Leszczyszyn-Pynka, M., Szata, W., Camacho, Ricardo J., Palma, C., Borges, F., Paixão, T., Duque, V., Araújo, F., Otelea, D., Paraschiv, S., Tudor, A. M., Cernat, R., Chiriac, C., Dumitrescu, F., Prisecariu, L. J., Stanojevic, M., Jevtovic, Dj, Salemovic, D., Stanekova, D., Habekova, M., Chabadová, Z., Drobkova, T., Bukovinova, P., Shunnar, A., Truska, P., Poljak, M., Lunar, M., Babic, Dunja Z., Tomazic, J., Vidmar, L., Vovko, T., Karner, P., Garcia, F., Paredes, R., Monge, S., Moreno, S., del Amo, J., Asensi, V., Sirvent, J. L., de Mendoza, C., Delgado, R., Gutiérrez, F., Berenguer, J., Garcia-Bujalance, S., Stella, Natalia C., de, los Santos, Blanco, J. R., Dalmau, D., Rivero, M., Segura, F., Elıás, Marıá Jesús Pérez, Alvarez, M., Chueca, N., Rodríguez-Martín, C., Vidal, C., Palomares, J. C., Viciana, I., Viciana, P., Cordoba, J., Aguilera, A., Domingo, P., Galindo, M. J., Miralles, C., del Pozo, M. A., Ribera, E., Iribarren, J. A., Ruiz, L., de, la Torre, Vidal, F., Clotet, B., Heidarian, A., Aperia-Peipke, K., Axelsson, M., Mild, M., Karlsson, A., Sönnerborg, A., Thalme, A., Navér, L., Bratt, G., Blaxhult, A., Gisslén, M., Svennerholm, B., Bergbrant, I., Björkman, Per, Säll, C., Mellgren, Å., Lindholm, A., Kuylenstierna, N., Montelius, R., Azimi, F., Johansson, B., Carlsson, M., Johansson, E., Ljungberg, B., Ekvall, H., Strand, A., Mäkitalo, S., Öberg, S., Holmblad, P., Höfer, M., Holmberg, H., Josefson, P., Ryding, U., Van Kessel, A., Clinical sciences, Microbiology and Infection Control, Supporting clinical sciences, Clinicum, Department of Medicine, Virology, Cohorte de Adultos de la Red de Investigación en SIDA, Spain., SPREAD Program, [Hofstra,LM, Sauvageot,N, Struck,D, Schmit,JC ] Luxembourg Institute of Health, Luxembourg. [Hofstra,LM, Wensing,AMJ] Department of Virology, University Medical Center Utrecht, The Netherlands. [Albert,J, Sönnerborg,A] Karolinska Institute, Solna. Karolinska University Hospital, Stockholm, Sweden. [Alexiev,I, Beshkov,D] National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria. [Garcia,F] Complejo Hospitalario Universitario de Granada. Instituto de Investigación IBS Granada, Spain. [Van de Vijver,DAMC, Boucher,CAB] Erasmus MC, University Medical Center, Rotterdam, The Netherlands. [Åsjö,B] University of Bergen, Norway. [Coughlan,S] University College Dublin, Ireland. [Descamps,D] AP-HP Groupe hospitalier Bichat-Claude Bernard. IAME INSERM UMR 1137. Université Paris Diderot Sorbonne Paris Cité, Paris, France. [Griskevicius,A] Lithuanian AIDS Center, Vilnius, Lithuania. [Hamouda,O] Robert Koch Institute, Berlin, Germany. [Horban,A] Hospital of Infectious Diseases, Warsaw, Poland. [Van Kasteren,M] St Elisabeth Hospital, Tilburg, The Netherlands. [Kolupajeva,T] Infectiology Center of Latvia, Riga. [Kostrikis,LG] University of Cyprus, Nicosia. [Liitsola,K] Department of Infectious Diseases, National Institute for Health and Welfare, Helsinki, Finland. [Linka,M] National Reference Laboratory for HIV/AIDS, National Institute of Public Health, Prague, Czech Republic. [Mor,O] National HIV Reference Laboratory, Chaim Sheba Medical Center, Tel-Hashomer, Israel. [Nielsen,C] Statens Serum Institut, Copenhagen, Denmark. [Otelea,D] National Institute for Infectious Diseases 'Prof. dr. Matei Bals', Bucharest, Romania. [Paraskevis,D] National Retrovirus Reference Center, University of Athens, Greece. [Paredes,R] IrsiCaixa Foundation, Badalona, Spain. [Poljak,M] Faculty of Medicine, Slovenian HIV/AIDS Reference Centre, University of Ljubljana, Slovenia. [Puchhammer-Stöckl,E] Medical University Vienna, Austria. [Staneková,D] Slovak Medical University, Bratislava, Slovakia. [Stanojevic,M] Faculty of Medicine, University of Belgrade, Serbia. [Van Laethem,K] Rega Institute for Medical Research, KU Leuven, Belgium. [Zazzi,M] University of Siena, Italy. [Zidovec Lepej,S] University Hospital for Infectious Diseases 'Dr. Fran Mihaljevic', Zagreb, Croatia., This work was supported by a CORE grant of Fond National de la Recherche Luxembourg (grant number C12/BM/4011111–HIV molecular epidemiology in Europe). This work has been partially supported by the European Commission (fifth framework, grant number QLK2-CT-2001-01344, sixth framework, grant number LSHP-CT-2006-518211, DynaNets grant number 233847, seventh framework, CHAIN grant number 223131), Belgium: Belgian AIDS Reference Laboratory Fund, Belgian Fonds voor Wetenschappelijk Onderzoek (grant number G.0692.14), Cyprus: Cyprus Research Promotion Foundation (grant number Health/0104/22), Denmark: Danish AIDS Foundation, France: Agence Nationale de Recherches sur le SIDA et les Hepatites Virales, Germany: Ministry of Health (grant number 1502-686-18), Ministry of Education and Research (grant number 01KI501), Italy: Fifth National Program on HIV/AIDS, Instituto Superiore di Sanità (grant numbers 40F.56 and 20D.1.6), Luxembourg: Fondation Recherche sur le SiDA and Ministry of Health, Republic of Serbia: Ministry of Education and Science (grant number 175024), Slovakia: project 'Center of Excellence of Environmental Health,' ITMS number 26240120033, based on supporting operational research and development program financed from the European Regional Development Fund, and Sweden: Swedish Research Council and Swedish Civil Contingencies Agency., APH - Health Behaviors & Chronic Diseases, Graduate School, Hofstra, LM, Sauvageot, N, Albert, J, Alexiev, I, Garcia, F, Struck, D, Van de Vijver, DA, Åsjö, B, Beshkov, D, Coughlan, S, Descamps, D, Griskevicius, A, Hamouda, O, Horban, A, Van Kasteren, M, Kolupajeva, T, Kostrikis, LG, Liitsola, K, Linka, M, Mor, O, Nielsen, C, Otelea, D, Paraskevis, D, Paredes, R, Poljak, M, Puchhammer-Stöckl, E, Sönnerborg, A, Staneková, D, Stanojevic, M, Van Laethem, K, Zazzi, M, Lepej, SZ, Boucher, CA, Schmit, JC, Wensing, AM, SPREAD program investigators, including Vitale F and Tramuto, F, Vandamme, Annemie, Vercauteren, Jurgen, Schrooten, Yoeri, Van Ranst, Marc, Van Wijngaerden, Eric, Derdelinckx, Inge, Camacho, Ricardo Jorge, Kostrikis, Leontios G. [0000-0002-5340-7109], and Paraskevis, Dimitrios [0000-0001-6167-7152]

Subjects
Male, Human immunodeficiency virus 1, Etravirine, RNA directed DNA polymerase inhibitor, darunavir, HIV Infections, Settore MED/42 - Igiene Generale E Applicata, Disciplines and Occupations::Health Occupations::Medicine::Public Health [Medical Subject Headings], Organisms::Eukaryota::Animals::Chordata::Vertebrates::Mammals::Primates::Haplorhini::Catarrhini::Hominidae::Humans [Medical Subject Headings], Salud pública, genetics, Inhibidores de proteasas, Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Epidemiologic Methods::Data Collection::Vital Statistics::Morbidity::Prevalence [Medical Subject Headings], atazanavir, media_common, transmission, Geographicals::Geographic Locations::Europe [Medical Subject Headings], 3. Good health, microbial sensitivity test, priority journal, Europe, HIV-1, antiretroviral therapy, drug resistance, HIV/AIDS, lamivudine, Reverse Transcriptase Inhibitors/pharmacology, anti human immunodeficiency virus agent, Drug, Microbiology (medical), medicine.medical_specialty, antiviral susceptibility, Phenomena and Processes::Genetic Phenomena::Genetic Variation::Mutation [Medical Subject Headings], media_common.quotation_subject, 030106 microbiology, HIV Infections/drug therapy, Chemicals and Drugs::Chemical Actions and Uses::Pharmacologic Actions::Therapeutic Uses::Anti-Infective Agents::Antiviral Agents::Anti-Retroviral Agents::Reverse Transcriptase Inhibitors [Medical Subject Headings], Microbial Sensitivity Tests, RILPIVIRINE, Article, EFAVIRENZ, 03 medical and health sciences, transmitted drug resistance, SDG 3 - Good Health and Well-being, Humans, Transmission, human, Phenomena and Processes::Physiological Phenomena::Pharmacological Phenomena::Drug Resistance [Medical Subject Headings], REVERSE-TRANSCRIPTASE INHIBITORS, Rilpivirina, INTEGRASE, MUTATIONS, abacavir, major clinical study, Virology, Infecciones por VIH, Regimen, Antiretroviral therapy, Drug resistance, Medicine (all), Infectious Diseases, chemistry, Chemicals and Drugs::Heterocyclic Compounds::Heterocyclic Compounds, 1-Ring::Oxazines::Benzoxazines [Medical Subject Headings], Mutation, 0301 basic medicine, nevirapine, Communicable diseases, Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Epidemiologic Methods::Statistics as Topic::Confidence Intervals [Medical Subject Headings], chemistry.chemical_compound, antiviral therapy, INFECTION, Medicine and Health Sciences, Prevalence, Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Epidemiologic Methods::Data Collection::Surveys and Questionnaires [Medical Subject Headings], Viral, Non-U.S. Gov't, Reverse-transcriptase inhibitor, antiretrovirus agent, Research Support, Non-U.S. Gov't, Human immunodeficiency virus infected patient, Middle Aged, virology, PREVALENCE, Encuestas y Cuestionarios, ANTIRETROVIRAL TREATMENT, HIV-1/drug effects, HIV Protease Inhibitors/pharmacology, Rilpivirine, Reverse Transcriptase Inhibitors, Diseases::Immune System Diseases::Immunologic Deficiency Syndromes::HIV Infections [Medical Subject Headings], Female, HIV drug resistance, medicine.drug, Adult, Human immunodeficiency virus proteinase inhibitor, Chemicals and Drugs::Organic Chemicals::Nitriles::Rilpivirine [Medical Subject Headings], Efavirenz, Anti-HIV Agents, Research Support, Resistencia a medicamentos, Settore MED/17 - MALATTIE INFETTIVE, antiviral resistance, Internal medicine, Anti-HIV Agents/pharmacology, Drug Resistance, Viral, Journal Article, medicine, Chemicals and Drugs::Chemical Actions and Uses::Pharmacologic Actions::Molecular Mechanisms of Pharmacological Action::Enzyme Inhibitors::Protease Inhibitors [Medical Subject Headings], abacavir plus lamivudine, Europa (Continente), HIV Protease Inhibitors, emtricitabine, nonhuman, Intervalos de confianza, Mutación, business.industry, HIV, prediction, Inhibidores de la transcriptasa inversa, Human immunodeficiency virus 1 infection, tenofovir, INDIVIDUALS, Drug Resistance, Viral/genetics, Benzoxazinas, ETRAVIRINE, drug effects, 3121 General medicine, internal medicine and other clinical medicine, Prevalencia, business
Abstract

Transmitted human immunodeficiency virus drug resistance in Europe is stable at around 8%. The impact of baseline mutation patterns on susceptibility to antiretroviral drugs should be addressed using clinical guidelines. The impact on baseline susceptibility is largest for nonnucleoside reverse transcriptase inhibitors., Background. Numerous studies have shown that baseline drug resistance patterns may influence the outcome of antiretroviral therapy. Therefore, guidelines recommend drug resistance testing to guide the choice of initial regimen. In addition to optimizing individual patient management, these baseline resistance data enable transmitted drug resistance (TDR) to be surveyed for public health purposes. The SPREAD program systematically collects data to gain insight into TDR occurring in Europe since 2001. Methods. Demographic, clinical, and virological data from 4140 antiretroviral-naive human immunodeficiency virus (HIV)–infected individuals from 26 countries who were newly diagnosed between 2008 and 2010 were analyzed. Evidence of TDR was defined using the WHO list for surveillance of drug resistance mutations. Prevalence of TDR was assessed over time by comparing the results to SPREAD data from 2002 to 2007. Baseline susceptibility to antiretroviral drugs was predicted using the Stanford HIVdb program version 7.0. Results. The overall prevalence of TDR did not change significantly over time and was 8.3% (95% confidence interval, 7.2%–9.5%) in 2008–2010. The most frequent indicators of TDR were nucleoside reverse transcriptase inhibitor (NRTI) mutations (4.5%), followed by nonnucleoside reverse transcriptase inhibitor (NNRTI) mutations (2.9%) and protease inhibitor mutations (2.0%). Baseline mutations were most predictive of reduced susceptibility to initial NNRTI-based regimens: 4.5% and 6.5% of patient isolates were predicted to have resistance to regimens containing efavirenz or rilpivirine, respectively, independent of current NRTI backbones. Conclusions. Although TDR was highest for NRTIs, the impact of baseline drug resistance patterns on susceptibility was largest for NNRTIs. The prevalence of TDR assessed by epidemiological surveys does not clearly indicate to what degree susceptibility to different drug classes is affected.

Published
2016

34. Segregation, precipitation, and \alpha-\alpha' phase separation in Fe-Cr alloys: a multi-scale modelling approach

Author

Kuronen, A., Heinonen, M. H., Granroth, S., Perälä, R. E., Kilpi, T., Laukkanen, P., Lång, J., Dahl, J., Punkkinen, M. P. J., Kokko, K., Ropo, M., Johansson, B., and Vitos, L.

Subjects
Condensed Matter - Materials Science
Abstract

Segregation, precipitation, and phase separation in Fe-Cr systems is investigated. Monte Carlo simulations using semiempirical interatomic potential, first-principles total energy calculations, and experimental spectroscopy are used. In order to obtain a general picture of the relation of the atomic interactions and properties of Fe-Cr alloys in bulk, surface, and interface regions several complementary methods has to be used. Using Exact Muffin-Tin Orbitals method the effective chemical potential as a function of Cr content (0-15 at.% Cr) is calculated for a surface, second atomic layer and bulk. At ~10 at.% Cr in the alloy the reversal of the driving force of a Cr atom to occupy either bulk or surface sites is obtained. The Cr containing surfaces are expected when the Cr content exceeds ~10 at.%. The second atomic layer forms about 0.3 eV barrier for the migration of Cr atoms between bulk and surface atomic layer. To get information on Fe-Cr in larger scales we use semiempirical methods. Using combined Monte Carlo molecular dynamics simulations, based on semiempirical potential, the precipitation of Cr into isolated pockets in bulk Fe-Cr and the upper limit of the solubility of Cr into Fe layers in Fe/Cr layer system is studied. The theoretical predictions are tested using spectroscopic measurements. Hard X-ray photoelectron spectroscopy and Auger electron spectroscopy investigations were carried out to explore Cr segregation and precipitation in Fe/Cr double layer and Fe_0.95Cr_0.05 and Fe_0.85Cr_0.15 alloys. Initial oxidation of Fe-Cr was investigated experimentally at 10^-8 Torr pressure of the spectrometers showing intense Cr_2O_3 signal. Cr segregation and the formation of Cr rich precipitates were traced by analysing the experimental spectral intensities with respect to annealing time, Cr content, and kinetic energy of the exited electron., Comment: 16 pages, 14 figures, 52 references

Published
2015

35. Segregation, precipitation, and ��-��' phase separation in Fe-Cr alloys: a multi-scale modelling approach

Author

Kuronen, A., Heinonen, M. H., Granroth, S., Per��l��, R. E., Kilpi, T., Laukkanen, P., L��ng, J., Dahl, J., Punkkinen, M. P. J., Kokko, K., Ropo, M., Johansson, B., and Vitos, L.

Subjects
Materials Science (cond-mat.mtrl-sci), FOS: Physical sciences
Abstract

Segregation, precipitation, and phase separation in Fe-Cr systems is investigated. Monte Carlo simulations using semiempirical interatomic potential, first-principles total energy calculations, and experimental spectroscopy are used. In order to obtain a general picture of the relation of the atomic interactions and properties of Fe-Cr alloys in bulk, surface, and interface regions several complementary methods has to be used. Using Exact Muffin-Tin Orbitals method the effective chemical potential as a function of Cr content (0-15 at.% Cr) is calculated for a surface, second atomic layer and bulk. At ~10 at.% Cr in the alloy the reversal of the driving force of a Cr atom to occupy either bulk or surface sites is obtained. The Cr containing surfaces are expected when the Cr content exceeds ~10 at.%. The second atomic layer forms about 0.3 eV barrier for the migration of Cr atoms between bulk and surface atomic layer. To get information on Fe-Cr in larger scales we use semiempirical methods. Using combined Monte Carlo molecular dynamics simulations, based on semiempirical potential, the precipitation of Cr into isolated pockets in bulk Fe-Cr and the upper limit of the solubility of Cr into Fe layers in Fe/Cr layer system is studied. The theoretical predictions are tested using spectroscopic measurements. Hard X-ray photoelectron spectroscopy and Auger electron spectroscopy investigations were carried out to explore Cr segregation and precipitation in Fe/Cr double layer and Fe_0.95Cr_0.05 and Fe_0.85Cr_0.15 alloys. Initial oxidation of Fe-Cr was investigated experimentally at 10^-8 Torr pressure of the spectrometers showing intense Cr_2O_3 signal. Cr segregation and the formation of Cr rich precipitates were traced by analysing the experimental spectral intensities with respect to annealing time, Cr content, and kinetic energy of the exited electron., 16 pages, 14 figures, 52 references

Published
2015
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36. Ab initio phonon calculations for Ll(2) Ni3Al and B2NiAl

Author

Isaeva, E.I., Lichtenstein, A.I., Vekilov, Y.K., Smirnova, E.A., Abrikosov, I.A., Simak, S.I., Ahuja, R., and Johansson, B.

Subjects
Condensed Matter::Materials Science, Theory of Condensed Matter, Condensed Matter::Superconductivity, Condensed Matter::Strongly Correlated Electrons
Abstract

Item does not contain fulltext The phonon spectra and phonon density of states of the Ni3Al and NiAl intermetallic compounds are calculated from first principles using the linear response method in conjunction with ultrasoft pseudopotentials. The calculated phonon dispersion curves are in good agreement with available experimental results from inelastic neutron scattering. (C) 2003 Elsevier Ltd. All rights reserved.

Published
2004

37. Increase in transmitted resistance to non-nucleoside reverse transcriptase inhibitors among newly diagnosed HIV-1 infections in Europe

Author

Moutschen, M., Frentz, D., Van de Vijver, D. A. M. C., Abecasis, A. B., Albert, Jan, Hamouda, O., Jørgensen, L. B., Ku¨cherer, C., Struck, D., Schmit, J. -C, Vercauteren, J., A˚sjo¨, B., Balotta, Claudia, Beshkov, Danail, Camacho, Ricardo J., Clotet, B., Coughlan, S., Griskevicius, A., Grossman, Z., Horban, A., Kolupajeva, T., Korn, K., Kostrikis, Leontios G., Liitsola, K., Linka, M., Nielsen, C., Otelea, D., Paraskevis, Dimitrios N., Paredes, R., Poljak, M., Puchhammer, Stockl E., So¨nnerborg, A., Stanekova, D., Stanojevic, M., Van Wijngaerden, E., Wensing, A. M. J., Boucher, C. A. B., Sarcletti, M., Schmied, B., Geit, M., Balluch, G., Vandamme, A. -M, Derdelinckx, I., Sasse, A., Bogaert, M., Ceunen, H., De Roo, A., De Wit, S., Echahidi, F., Fransen, K., Goffard, J. -C, Goubau, P., Goudeseune, E., Yombi, J. -C, Lacor, P., Liesnard, C., Pierard, D., Rens, R., Schrooten, Y., Vaira, D., Vandekerckhove, L. P. R., Van den Heuvel, A., Van Der Gucht, B., Van Ranst, M., Vandercam, B., Vekemans, M., Verhofstede, C., Clumeck, N., Van Laethem, K., Demetriades, Ioannis, Kousiappa, Ioanna, Demetriou, Victoria L., Hezka, Johana, Bruckova, M., Machala, L., Gerstoft, J., Mathiesen, L., Pedersen, C., Nielsen, H., Laursen, A., Kvinesdal, B., Salminen, M., Ristola, M., Suni, J., Sutinen, J., Berg, T., Braun, P., Poggensee, G., Da¨umer, M., Eberle, J., Heiken, H., Kaiser, R., Knechten, H., Mu¨ller, H., Neifer, S., Schmidt, B., Walter, H., Gunsenheimer-Bartmeyer, B., Harrer, T., Hatzakis, Angelos E., Magiorkinis, Emmanouil N., Hatzitheodorou, Eleni, Haida, Catherine, Zavitsanou, Assimina, Magiorkinis, Gkikas, Lazanas, Marios C., Chini, Maria C., Magafas, N., Tsogas, Nickolaos, Paparizos, Vassilios A., Kourkounti, Sofia, Antoniadou, Anastasia C., Papadopoulos, Antonios I., Panagopoulos, Periklis, Poulakou, Garyphallia G., Sakka, V., Chryssos, Georgios, Drimis, Stylianos, Gargalianos, Panagiotis, Lelekis, Moyssis I., Chilomenos, G., Psichogiou, Mina A., Daikos, George L., Panos, George, Haratsis, G., Kordossis, Theodore, Kontos, Athanasios N., Koratzanis, Georgios, Theodoridou, Maria C., Mostrou, Glykeria J., Spoulou, Vana I., De Gascun, C., Byrne, C., Duffy, M., Bergin, C., Reidy, D., Farrell, G., Lambert, J., O'Connor, E., Rochford, A., Low, J., Coakely, P., O'Dea, S., Hall, W., Levi, I., Chemtob, D., Riva, C., Mussini, C., Caramma, I., Capetti, A., Colombo, M. C., Rossi, C., Prati, F., Tramuto, F., Vitale, F., Ciccozzi, M., Angarano, G., Rezza, G., Schmit, J. C., Hemmer, R., Arendt, V., Staub, T., Schneider, F., Roman, F., van Kessel, A., van Bentum, P. H. M., Brinkman, K., op de Coul, E. L., van der Ende, M. E., Hoepelman, I., van Kasteren, M., Juttmann, J., Kuipers, M., Langebeek, N., Richter, C., Santegoets, R., Schrijnders-Gudde, L., Schuurman, R., van de Ven, B. J. M., Ormaasen, V., Aavitsland, P., Stanczak, J. J., Stanczak, G. P., Firlag-Burkacka, E., Wiercinska-Drapalo, A., Jablonowska, E., Malolepsza, E., Leszczyszyn-Pynka, M., Szata, W., Palma, C., Borges, F., Paixa&tild, o, T., Duque, V., Araújo, F., Jevtovic, D., Salemovic, D., Habekova, M., Mokráš, Miloš, Truska, P., Lunar, M., Babic, Dunja Z., Tomazic, J., Vidmar, L., Vovko, T., Karner, P., Domingo, P., Galindo, M. J., Miralles, C., del Pozo, M. A., Ribera, E., Iribarren, J. A., Ruiz, L., de la Torre, J., Vidal, F., Garcia, F., Heidarian, A., Aperia-Peipke, K., Axelsson, M., Mild, M., Karlsson, A., Thalme, A., Nave´r, L., Bratt, G., Blaxhult, A., Gissle´n, M., Svennerholm, B., Bergbrant, I., Björkman, Per, Sa¨ll, C., Mellgren, A˚, Lindholm, A., Kuylenstierna, N., Montelius, R., Azimi, F., Johansson, B., Carlsson, M., Johansson, E., Ljungberg, B., Ekvall, H., Strand, A., Ma¨kitalo, S., o¨berg, S., Holmblad, P., Ho¨fer, M., Holmberg, H., Josefson, P., Ryding, U., Van Kessel, A., Kostrikis, Leontios G. [0000-0002-5340-7109], Paraskevis, Dimitrios [0000-0001-6167-7152], Virology, Erasmus MC other, Frentz, Dineke, Van de Vijver, David A.M.C., Abecasis, Ana B., Albert, Jan, Hamouda, Osamah, Jørgensen, Louise B., Ku¨cherer, Claudia, Struck, Daniel, Schmit, Jean-Claude, Vercauteren, Jurgen, A˚sjo¨, Birgitta, Balotta, Claudia, Beshkov, Danail, Camacho, Ricardo J., Clotet, Bonaventura, Coughlan, Suzie, Griskevicius, Algirda, Grossman, Zehava, Horban, Andrzej, Kolupajeva, Tatjana, Korn, Klau, Kostrikis, Leondios G., Liitsola, Kirsi, Linka, Marek, Nielsen, Clau, Otelea, Dan, Paraskevis, Dimitrio, Paredes, Roger, Poljak, Mario, Puchhammer-Sto¨ckl, Elisabeth, So¨nnerborg, Ander, Stanekova, Danica, Stanojevic, Maja, Van Wijngaerden, Eric, Wensing, Annemarie M.J., Boucher, Charles A.B., SPREAD programme investigators, including Vitale F and Tramuto F., Graduate School, UCL - SSS/IREC/MBLG - Pôle de Microbiologie médicale, UCL - (SLuc) Service de microbiologie, UCL - (SLuc) Service de médecine interne générale, UCL - (SLuc) Service d'hématologie, Clinicum, and Department of Medicine

Subjects
Male, virus strain, Resistance, HIV Infections, Drug resistance, THERAPY, Nucleoside Reverse Transcriptase Inhibitor, ANTIRETROVIRAL DRUG-RESISTANCE, 0302 clinical medicine, Medical microbiology, Genotype, Medicine and Health Sciences, Prevalence, HIV Infection, 030212 general & internal medicine, UNITED-KINGDOM, Phylogeny, 0303 health sciences, Communicable disease, Transmission (medicine), adult, virus mutation, UPDATED RECOMMENDATIONS, virus transmission, 3. Good health, Europe, Infectious Diseases, female, risk factor, virus resistance, Female, NAIVE PATIENTS, SOCIETY-USA PANEL, Research Article, Human, Adult, medicine.medical_specialty, Anti-HIV Agents, Virus, Article, 03 medical and health sciences, SDG 3 - Good Health and Well-being, male, MOLECULAR EPIDEMIOLOGY, Drug Resistance, Viral, medicine, proteinase inhibitor, Humans, Transmission, controlled study, human, molecular phylogeny, 030304 developmental biology, nonhuman, MUTATIONS, business.industry, Anti-HIV Agent, nucleotide sequence, nonnucleoside reverse transcriptase inhibitor, Human immunodeficiency virus 1 infection, Virology, major clinical study, unindexed sequence, Parasitology, 3121 General medicine, internal medicine and other clinical medicine, Mutation, HIV-1, business
Abstract

Background: One out of ten newly diagnosed patients in Europe was infected with a virus carrying a drug resistant mutation. We analysed the patterns over time for transmitted drug resistance mutations (TDRM) using data from the European Spread program.Methods: Clinical, epidemiological and virological data from 4317 patients newly diagnosed with HIV-1 infection between 2002 and 2007 were analysed. Patients were enrolled using a pre-defined sampling strategy.Results: The overall prevalence of TDRM in this period was 8.9% (95% CI: 8.1-9.8). Interestingly, significant changes over time in TDRM caused by the different drug classes were found. Whereas nucleoside resistance mutations remained constant at 5%, a significant decline in protease inhibitors resistance mutations was observed, from 3.9% in 2002 to 1.6% in 2007 (p = 0.001). In contrast, resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs) doubled from 2.0% in 2002 to 4.1% in 2007 (p = 0.004) with 58% of viral strains carrying a K103N mutation. Phylogenetic analysis showed that these temporal changes could not be explained by large clusters of TDRM.Conclusion: During the years 2002 to 2007 transmitted resistance to NNRTI has doubled to 4% in Europe. The frequent use of NNRTI in first-line regimens and the clinical impact of NNRTI mutations warrants continued monitoring. © 2014 Frentz et al. licensee BioMed Central Ltd. 14 Cited By :16

Published
2014

38. Increase in transmitted resistance to non-nucleoside reverse transcriptase inhibitors among newly diagnosed HIV-1 infections in Europe

Author

Frentz, D. Van de Vijver, D.A.M.C. Abecasis, A.B. Albert, J. Hamouda, O. Jørgensen, L.B. Kücherer, C. Struck, D. Schmit, J.-C. Vercauteren, J. Åsjö, B. Balotta, C. Beshkov, D. Camacho, R.J. Clotet, B. Coughlan, S. Griskevicius, A. Grossman, Z. Horban, A. Kolupajeva, T. Korn, K. Kostrikis, L.G. Liitsola, K. Linka, M. Nielsen, C. Otelea, D. Paraskevis, D. Paredes, R. Poljak, M. Puchhammer-Stöckl, E. Sönnerborg, A. Stanekova, D. Stanojevic, M. Van Wijngaerden, E. Wensing, A.M.J. Boucher, C.A.B. Puchhammer-Stockl, E. Sarcletti, M. Schmied, B. Geit, M. Balluch, G. Vandamme, A.-M. Vercauteren, J. Derdelinckx, I. Sasse, A. Bogaert, M. Ceunen, H. De Roo, A. De Wit, S. Echahidi, F. Fransen, K. Goffard, J.-C. Goubau, P. Goudeseune, E. Yombi, J.-C. Lacor, P. Liesnard, C. Moutschen, M. Pierard, D. Rens, R. Schrooten, Y. Vaira, D. Vandekerckhove, L.P.R. Van den Heuvel, A. Van Der Gucht, B. Van Ranst, M. Vandercam, B. Vekemans, M. Verhofstede, C. Clumeck, N. Van Laethem, K. Demetriades, I. Kousiappa, I. Demetriou, V. Hezka, J. Bruckova, M. Linka, M. Machala, L. Nielsen, C. Jørgensen, L.B. Gerstoft, J. Mathiesen, L. Pedersen, C. Nielsen, H. Laursen, A. Kvinesdal, B. Salminen, M. Ristola, M. Liitsola, K. Suni, J. Sutinen, J. Korn, K. Kücherer, C. Berg, T. Braun, P. Poggensee, G. Däumer, M. Eberle, J. Heiken, H. Kaiser, R. Knechten, H. Müller, H. Neifer, S. Schmidt, B. Walter, H. Gunsenheimer-Bartmeyer, B. Harrer, T. Paraskevis, D. Hatzakis, A. Magiorkinis, E. Hatzitheodorou, E. Haida, C. Zavitsanou, A. Magiorkinis, G. Lazanas, M. Chini, M. Magafas, N. Tsogas, N. Paparizos, V. Kourkounti, S. Antoniadou, A. Papadopoulos, A. Panagopoulos, P. Poulakou, G. Sakka, V. Chryssos, G. Drimis, S. Gargalianos, P. Lelekis, M. Chilomenos, G. Psichogiou, M. Daikos, G.L. Panos, G. Haratsis, G. Kordossis, T. Kontos, A. Koratzanis, G. Theodoridou, M. Mostrou, G. Spoulou, V. Coughlan, S. De Gascun, C. Byrne, C. Duffy, M. Bergin, C. Reidy, D. Farrell, G. Lambert, J. O'Connor, E. Rochford, A. Low, J. Coakely, P. O'Dea, S. Hall, W. Grossman, Z. Levi, I. Chemtob, D. Balotta, C. Riva, C. Mussini, C. Caramma, I. Capetti, A. Colombo, M.C. Rossi, C. Prati, F. Tramuto, F. Vitale, F. Ciccozzi, M. Angarano, G. Rezza, G. Schmit, J.C. Struck, D. Hemmer, R. Arendt, V. Staub, T. Schneider, F. Roman, F. Wensing, A.M.J. Boucher, C.A.B. van Kessel, A. van Bentum, P.H.M. Brinkman, K. op de Coul, E.L. van der Ende, M.E. Hoepelman, I. van Kasteren, M. Juttmann, J. Kuipers, M. Langebeek, N. Richter, C. Santegoets, R. Schrijnders-Gudde, L. Schuurman, R. van de Ven, B.J.M. Åsjö, B. Ormaasen, V. Aavitsland, P. Horban, A. Stanczak, J.J. Stanczak, G.P. Firlag-Burkacka, E. Wiercinska-Drapalo, A. Jablonowska, E. Malolepsza, E. Leszczyszyn-Pynka, M. Szata, W. Camacho, R. Palma, C. Borges, F. Paixão, T. Duque, V. Araújo, F. Jevtovic, D. Salemovic, D. Stanekova, D. Habekova, M. Mokras, M. Truska, P. Poljak, M. Lunar, M. Babic, D. Tomazic, J. Vidmar, L. Vovko, T. Karner, P. Clotet, B. Domingo, P. Galindo, M.J. Miralles, C. del Pozo, M.A. Ribera, E. Iribarren, J.A. Ruiz, L. de la Torre, J. Vidal, F. Garcia, F. Paredes, R. Albert, J. Heidarian, A. Aperia-Peipke, K. Axelsson, M. Mild, M. Karlsson, A. Sönnerborg, A. Thalme, A. Navér, L. Bratt, G. Karlsson, A. Blaxhult, A. Gisslén, M. Svennerholm, B. Bergbrant, I. Björkman, P. Säll, C. Mellgren, Å. Lindholm, A. Kuylenstierna, N. Montelius, R. Azimi, F. Johansson, B. Carlsson, M. Johansson, E. Ljungberg, B. Ekvall, H. Strand, A. Mäkitalo, S. öberg, S. Holmblad, P. Höfer, M. Holmberg, H. Josefson, P. Ryding, U. on behalf of the SPREAD Programme

Abstract

Background: One out of ten newly diagnosed patients in Europe was infected with a virus carrying a drug resistant mutation. We analysed the patterns over time for transmitted drug resistance mutations (TDRM) using data from the European Spread program.Methods: Clinical, epidemiological and virological data from 4317 patients newly diagnosed with HIV-1 infection between 2002 and 2007 were analysed. Patients were enrolled using a pre-defined sampling strategy.Results: The overall prevalence of TDRM in this period was 8.9% (95% CI: 8.1-9.8). Interestingly, significant changes over time in TDRM caused by the different drug classes were found. Whereas nucleoside resistance mutations remained constant at 5%, a significant decline in protease inhibitors resistance mutations was observed, from 3.9% in 2002 to 1.6% in 2007 (p = 0.001). In contrast, resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs) doubled from 2.0% in 2002 to 4.1% in 2007 (p = 0.004) with 58% of viral strains carrying a K103N mutation. Phylogenetic analysis showed that these temporal changes could not be explained by large clusters of TDRM.Conclusion: During the years 2002 to 2007 transmitted resistance to NNRTI has doubled to 4% in Europe. The frequent use of NNRTI in first-line regimens and the clinical impact of NNRTI mutations warrants continued monitoring. © 2014 Frentz et al.; licensee BioMed Central Ltd.

Published
2014

39. Enzyme immunoassay for rat C-peptide

Author

LI, Ling, OSHIDA, Yoshiharu, LUO, Weiquan, NAKAO, Titose, JOHANSSON, B-L., WAHREN, J., YANAIHARA, Noboru, and SATO, Yuzo

Abstract

Our previous studies suggest that C-peptide augments glucose utilization in diabetic rats. However, a reliable assay for rat C-peptide has not been available. In the present study, a sensitive and specific enzyme immunoassay for rat C-peptide has been developed. Effects of rat, pig, goat and fetal bovine sera on the standard curve were studied, and did not produced significant displacement. Rat C-peptide standard concentration ranged from 0.024-100 ng/ml. The intraassy coefficient of variation (CV) was 3.9 ± 2.2% (less than 8%). The fasting and postprandial plasma C-peptide level in normal rat were 6.89 ng/ml and 13.28 ng/ml, respectively. Rat plasma C-peptide levels following oral glucose tolerance test in normal rats were consistent with expected patterns. In conclusion, we have developed and validated a rat C-peptide enzyme immunoassay that is sensitive and simple for rat C-peptide in plasma. This assay provides a reliable tool for studies of diabetes using rat models.

Published
1997

41. Hexagonal flow v_6 as a superposition of elliptic v_2 and triangular v_3 flows

Author

Bravina, L. V., Johansson, B. H. Brusheim, Eyyubova, G. Kh., Korotkikh, V. L., Lokhtin, I. P., Malinina, L. V., Petrushanko, S. V., Snigirev, A. M., and Zabrodin, E. E.

Subjects
Nuclear Theory (nucl-th), High Energy Physics - Phenomenology, High Energy Physics - Phenomenology (hep-ph), Nuclear Theory, FOS: Physical sciences, Nuclear Experiment (nucl-ex), Nuclear Experiment
Abstract

Partial contributions of elliptic v_2 and triangular v_3 flows to the hexagonal v_6 flow are studied within the HYDJET++ model for Pb+Pb collisions at sqrt{s}=2.76 TeV. Scaling of the ratio v_6^{1/6}{Psi_2} / v_2^{1/2}{Psi_2} in the elliptic flow plane, Psi_2, is predicted in the range 1 < p_T < 4 GeV/c for semicentral and semiperipheral collisions. Jets increase this ratio by about 10% and also cause its rise at p_T > 3.5 GeV/c. The part of v_6 coming from v_2 is instantly increasing as the reaction becomes more peripheral, whereas the contribution of v_3 to v_6 drops. This behavior explains the experimentally observed increase of correlations between second and sixth harmonics and decrease of correlations between third and sixth harmonics with rising impact parameter $b$. Our study favors the idea that basic features of the hexagonal flow can be understood in terms of the interplay of elliptic and triangular flows., Final version

Published
2013

42. Limited cross-border infections in patients newly diagnosed with HIV in Europe

Author

Moutschen, M., Frentz, D., Wensing, A. M. J., Albert, Jan, Paraskevis, Dimitrios N., Abecasis, A. B., Hamouda, O., Jørgensen, L. B., Kücherer, C., Struck, D., Schmit, J. -C, Åsjö, Birgitta, Balotta, Claudia, Beshkov, Danail, Camacho, Ricardo J., Clotet, B., Coughlan, S., De Wit, S., Griskevicius, A., Grossman, Z., Horban, A., Kolupajeva, T., Korn, K., Kostrikis, Leontios G., Liitsola, K., Linka, M., Nielsen, C., Otelea, D., Paredes, R., Poljak, M., Puchhammer-Stöckl, E., Sönnerborg, A., Stanekova, D., Stanojevic, M., Vandamme, A. -M, Boucher, C. A. B., Van de Vijver, D. A. M. C., Balluch, G., Vercauteren, J., Derdelinckx, I., Sasse, A., Bogaert, M., Ceunen, H., De Roo, A., Echahidi, F., Fransen, K., Goffard, J. -C, Goubau, P., Goudeseune, E., Yombi, J. -C, Lacor, P., Liesnard, C., Pierard, D., Rens, R., Schrooten, Y., Vaira, D., Vandekerckhove, L. P. R., Van den Heuvel, A., Van Der Gucht, B., Van Ranst, M., Van Wijngaerden, E., Vandercam, B., Vekemans, M., Verhofstede, C., Clumeck, N., Van Laethem, K., Demetriades, Ioannis, Kousiappa, Ioanna, Demetriou, Victoria L., Hezka, Johana, Bruckova, M., Machala, L., Gerstoft, J., Mathiesen, L., Pedersen, C., Nielsen, H., Laursen, A., Kvinesdal, B., Salminen, M., Ristola, M., Suni, J., Sutinen, J., Berg, T., Braun, P., Poggensee, G., Däumer, M., Eberle, J., Heiken, H., Kaiser, R., Knechten, H., Müller, H., Neifer, S., Schmidt, B., Walter, H., Gunsenheimer-Bartmeyer, B., Harrer, T., Hatzakis, Angelos E., Magiorkinis, Emmanouil N., Hatzitheodorou, Eleni, Haida, Catherine, Zavitsanou, Assimina, Magiorkinis, Gkikas, Lazanas, Marios C., Chini, Maria C., Magafas, N., Tsogas, Nickolaos, Paparizos, Vassilios A., Kourkounti, Sofia, Antoniadou, Anastasia C., Papadopoulos, Antonios I., Panagopoulos, Periklis, Poulakou, Garyphallia G., Sakka, V., Chryssos, Georgios, Drimis, Stylianos, Gargalianos, Panagiotis, Lelekis, Moyssis I., Chilomenos, G., Psichogiou, Mina A., Daikos, George L., Panos, George, Haratsis, G., Kordossis, Theodore, Kontos, Athanasios N., Koratzanis, Georgios, Theodoridou, Maria C., Mostrou, Glykeria J., Spoulou, Vana I., De Gascun, C., Byrne, C., Duffy, M., Bergin, C., Reidy, D., Farrell, G., Lambert, J., O'Connor, E., Rochford, A., Low, J., Coakely, P., O'Dea, S., Hall, W., Levi, I., Chemtob, D., Franzetti, M., Lai, A., Binda, F., Tramuto, F., Ciccozzi, M., Mussini, C., Angarano, G., Rezza, G., Schmit, J. C., Hemmer, R., Arendt, V., Staub, T., Schneider, F., Roman, F., van Kessel, A., van Bentum, P. H. M., Brinkman, K., de Coul, E. L., van der Ende, M. E., Hoepelman, I. M., van Kasteren, M., Juttmann, J., Kuipers, M., Langebeek, N., Richter, C., Santegoets, R. M. W. J., Schrijnders-Gudde, L., Schuurman, R., van de Ven, B. J. M., Ormaasen, V., Aavitsland, P., Stanczak, J. J., Stanczak, G. P., Firlag-Burkacka, E., Wiercinska-Drapalo, A., Jablonowska, E., Malolepsza, E., Leszczyszyn-Pynka, M., Szata, W., Palma, C., Borges, F., Paixão, T., Duque, V., Araújo, F., Jevtovic, D., Salemovic, D., Habekova, M., Mokráš, Miloš, Truska, P., Lunar, M., Babic, Dunja Z., Tomazic, J., Vidmar, L., Vovko, T., Karner, P., Domingo, P., Galindo, M. J., Miralles, C., del Pozo, M. A., Ribera, E., Iribarren, J. A., Ruiz, L., de la Torre, J., Vidal, F., Garcia, F., Heidarian, A., Aperia-Peipke, K., Axelsson, M., Mild, M., Karlsson, A., Thalme, A., Navér, L., Bratt, G., Blaxhult, A., Gisslén, M., Svennerholm, B., Bergbrant, I., Björkman, Per, Säll, C., Mellgren, Å., Lindholm, A., Kuylenstierna, N., Montelius, R., Azimi, F., Johansson, B., Carlsson, M., Johansson, E., Ljungberg, B., Ekvall, H., Strand, A., Mäkitalo, S., öberg, S., Holmblad, P., Höfer, M., Holmberg, H., Josefson, P., Ryding, U., Van Kessel, A., Instituto de Higiene e Medicina Tropical (IHMT), Centro de Malária e outras Doenças Tropicais (CMDT), Clinicum, Department of Medicine, Infektiosairauksien yksikkö, Frentz, D, Wensing, AMJ, Albert, J, Paraskevis, D, Abecasis, AB, Hamouda, O, Jørgensen, LB, Kücherer, C, Struck, D, Schmit, JC, Åsjö, B, Balotta, C, Beshkov, D, Camacho, RJ, Clotet, B, Coughlan, S, De Wit, S, Griskevicius, A, Grossman, Z, Horban, A, Kolupajeva, T, Korn, K, Kostrikis, LG, Liitsola, K, Linka, M, Nielsen, C, Otelea, D, Paredes, R, Poljak, M, Puchhammer-Stöckl, E, Sönnerborg, A, Stanekova, D, Stanojevic, M, Vandamme, AM, Boucher, CAB, Van de Vijver, DAMC, Tramuto, F, Van Wijngaerden, Eric, Van Ranst, Marc, Van Laethem, Kristel, Derdelinckx, Inge, Kostrikis, Leontios G. [0000-0002-5340-7109], Paraskevis, Dimitrios [0000-0001-6167-7152], Virology, and Graduate School

Subjects
Male, Epidemiology, Human immunodeficiency virus (HIV), Human immunodeficiency virus 1, HIV Infections, medicine.disease_cause, Virologie générale, phylogeny, Settore MED/42 - Igiene Generale E Applicata, Men who have sex with men, EMERGENCE, 0302 clinical medicine, Medicine and Health Sciences, Medicine, Infection control, Cluster Analysis, 030212 general & internal medicine, Israel, Pathologie maladies infectieuses, travel, Phylogeny, 0303 health sciences, Molecular Epidemiology, Travel, Transmission (medicine), article, virus transmission, IMMUNODEFICIENCY-VIRUS TYPE-1, 3. Good health, Europe, female, Infectious Diseases, SUBTYPE B, DRUG-RESISTANT HIV-1, RNA, Viral, male homosexual, Adult, structural gene, Molecular Sequence Data, Newly diagnosed, Clusters, 03 medical and health sciences, male, SDG 3 - Good Health and Well-being, MOLECULAR EPIDEMIOLOGY, SWITZERLAND, Virology, geographic distribution, Humans, Transmission, In patient, human, 030304 developmental biology, nonhuman, Molecular epidemiology, business.industry, Research, high risk population, Virologie médicale, nucleotide sequence, Sequence Analysis, DNA, Human immunodeficiency virus 1 infection, major clinical study, unindexed sequence, 3121 General medicine, internal medicine and other clinical medicine, HIV-1, business, Europe, HIV-1, Transmission, Clusters, Demography, cluster analysis
Abstract

Background: International travel plays a role in the spread of HIV-1 across Europe. It is, however, not known whether international travel is more important for spread of the epidemic as compared to endogenous infections within single countries. In this study, phylogenetic associations among HIV of newly diagnosed patients were determined across Europe.Results: Data came from the SPREAD programme which collects samples of newly diagnosed patients that are representative for national HIV epidemics. 4260 pol sequences from 25 European countries and Israel collected in 2002-2007 were included.We identified 457 clusters including 1330 persons (31.2% of all patients). The cluster size ranged between 2 and 28. A number of 987 patients (74.2%) were part of a cluster that consisted only of patients originating from the same country. In addition, 135 patients (10.2%) were in a cluster including only individuals from neighboring countries. Finally, 208 patients (15.6%) clustered with individuals from countries without a common border. Clustering with patients from the same country was less prevalent in patients being infected with B subtype (P-value, SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2013

43. Effect of jets on $v_4/v_2^2$ ratio and constituent quark scaling in relativistic heavy-ion collisions

Author

Bravina, L., Johansson, B. H. Brusheim, Eyyubova, G., and Zabrodin, E.

Subjects
Nuclear Theory (nucl-th), High Energy Physics - Phenomenology, High Energy Physics - Phenomenology (hep-ph), Nuclear Theory, FOS: Physical sciences, High Energy Physics::Experiment, Nuclear Experiment (nucl-ex), Nuclear Experiment
Abstract

The Monte Carlo HYDJET++ model, that combines parametrized hydrodynamics with jets, is employed to study formation of second v_2 and fourth v_4 components of the anisotropic flow in ultrarelativistic heavy-ion collisions at energies of the Relativistic Heavy Ion Collider (RHIC) and the Large Hadron Collider (LHC), sqrt{s}=200 AGeV and sqrt{s}=2.76 ATeV, respectively. It is shown that the quenched jets contribute to the soft part of the v_2(p_T) and v_4(p_T) spectra. The jets increase the ratio v_4/v_2^2 thus leading to deviations of the ratio from the value of 0.5 predicted by the ideal hydrodynamics. Together with the event-by-event fluctuations, the influence of jets can explain quantitatively the ratio v_4/v_2^2 at p_T < 2 GeV/c for both energies and qualitatively the rise of its high-p_T tail at LHC. Jets are also responsible for violation of the number-of-constituent-quark (NCQ) scaling at LHC despite the fact that the scaling is fulfilled for the hydro-part of particle spectra., minor corrections, as published in Phys. Rev. C

Published
2013
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44. Polycentric urban trajectories and urban cultural economy

Author

Deinema, M., Kloosterman, R., Klaesson, J., Johansson, B., Karlsson, C., and Geographies of Globalizations (GoG, AISSR, FMG)

Abstract

This chapter traces the urban employment trends in cultural industries in the Netherlands from 1899 onwards and argues that a historical approach is necessary to understand economic geographical patterns in this post-industrial growth sector. Longitudinal employment data for the country’s four main cities, as well as case-study information on the spatial and institutional development of separate cultural industries in the Netherlands, reveal long-term intercity hierarchies of performance and historically-rooted local specializations. The effects of historical local trajectories on the inter-urban distribution of Dutch cultural production are weighed against more volatile factors such as creative class densities. Implications for the general outlook and development of these post-industrial urban economies are then explored, whereby the connectivity of the cities in international and regional networks is taken into account. The chapter concludes with identifying the evolutionary mechanisms at work in Dutch cultural industries and the value of a historical perspective vis-à-vis other geographical approaches to the urban cultural economy. As the four examined Dutch cities are all part of the Randstad megacity region, the dynamic Dutch urban cultural economy represents an unlikely case for stable inequalities between cities based on local trajectories. Consequently, strong implications may be inferred for cultural industry dynamics in other contexts.

Published
2013

46. Quantitative in-cylinder fuel measurements in a heavy duty diesel engine using structured laser illumination planar imaging (SLIPI)

Author

Sjöholm, J., Chartier, C., Kristensson, E., Berrocal, E., Gallo, Y., Mattias Richter, Andersson, Ö, Aldén, M., and Johansson, B.

Subjects
SLIPI, Heavy duty diesel engine, Fuel-jet, Jet-wall interactions, Quantitative LIF, Energy Engineering
Abstract

Laser-induced fluorescence (LIF) for quantitative fuel concentration measurements in a combustion engine is a challenging task. Measuring close to the walls of the combustion chamber is even more challenging as both the incident laser light and the signal are strongly reflected on the walls of the combustion chamber. By using a new technique called Structured Laser Illumination Planar Imaging (SLIPI) such background effects, as well as unwanted multiply scattered light, can be suppressed allowing for higher measurement accuracy. In this article we demonstrate, for the first time, the feasibility of the SLIPI technique for gas phase LIF and in-cylinder measurements. Results from regular LIF and SLIPI measurements are also compared. The measurements were made on a non-reacting fuel-jet with acetone as a fuel tracer in a heavy duty diesel engine (Scania D12). It is observed that the equivalence ratio measured by SLIPI in the free part of the jet is only two thirds of that measured by regular LIF during the early jet development.

Published
2012

47. Treatment-associated polymorphisms in protease are significantly associated with higher viral load and lower CD4 count in newly diagnosed drug-naive HIV-1 infected patients

Author

Moutschen, M., Theys, K., Deforche, K., Vercauteren, J., Libin, P., van de Vijver, D. A. M. C., Albert, Jan, Åsjö, Birgitta, Balotta, Claudia, Bruckova, M., Camacho, Ricardo J., Clotet, B., Coughlan, S., Grossman, Z., Hamouda, O., Horban, A., Korn, K., Kostrikis, Leontios G., Kücherer, C., Nielsen, C., Paraskevis, Dimitrios N., Poljak, M., Puchhammer-Stockl, E., Riva, C., Ruiz, L., Liitsola, K., Schmit, J. -C, Schuurman, R., Sönnerborg, A., Stanekova, D., Stanojevic, M., Struck, D., Van Laethem, K., Wensing, A. M. J., Boucher, C. A. B., Vandamme, A. M., Sarcletti, M., Schmied, B., Geit, M., Balluch, G., Derdelinckx, I., Sasse, A., Bogaert, M., Ceunen, H., De Roo, A., De Wit, S., Echahidi, F., Fransen, K., Goffard, J. -C, Goubau, P., Goudeseune, E., Yombi, J. -C, Lacor, P., Liesnard, C., Pierard, D., Rens, R., Schrooten, Y., Vaira, D., Van den Heuvel, A., Van Der Gucht, B., Van Ranst, M., Van Wijngaerden, E., Vandercam, B., Vekemans, M., Verhofstede, C., Clumeck, N., Demetriades, Ioannis, Kousiappa, Ioanna, Demetriou, Victoria L., Hezka, Johana, Linka, M., Machala, L., Jrgensen, L. B., Gerstoft, J., Mathiesen, L., Pedersen, C., Nielsen, H., Laursen, A., Kvinesdal, B., Ristola, M., Suni, J., Sutinen, J., K̈ucherer, C., Berg, T., Braun, P., Poggensee, G., Däumer, M., Eberle, J., Heiken, H., Kaiser, R., Knechten, H., Müller, H., Neifer, S., Schmidt, B., Walter, H., Gunsenheimer-Bartmeyer, B., Harrer, T., Hatzakis, Angelos E., Magiorkinis, Emmanouil N., Hatzitheodorou, Eleni, Issaris, C., Haida, Catherine, Zavitsanou, Assimina, Magiorkinis, Gkikas, Lazanas, Marios C., Chini, Maria C., Magafas, N., Tsogas, Nickolaos, Paparizos, Vassilios A., Kourkounti, Sofia, Antoniadou, Anastasia C., Papadopoulos, Antonios I., Panagopoulos, Periklis, Poulakou, Garyphallia G., Sakka, V., Chryssos, Georgios, Drimis, Stylianos, Gargalianos, Panagiotis, Lelekis, Moyssis I., Xilomenos, G., Psichogiou, Mina A., Daikos, George L., Panos, George, Haratsis, G., Kordossis, Theodore, Kontos, Athanasios N., Koratzanis, Georgios, Theodoridou, Maria C., Mostrou, Glykeria J., Spoulou, Vana I., Hall, W., De Gascun, C., Byrne, C., Duffy, M., Bergin, C., Reidy, D., Farrell, G., Lambert, J., O'Connor, E., Rochford, A., Low, J., Coakely, P., Levi, I., Chemtob, D., Mussini, C., Caramma, I., Capetti, A., Colombo, M. C., Rossi, C., Prati, F., Tramuto, F., Vitale, F., Ciccozzi, M., Angarano, G., Rezza, G., Schmit, J. C., Hemmer, R., Arendt, V., Staub, T., Schneider, F., Roman, F., van Bentum, P. H. M., Brinkman, K., op de Coul, E. L., van der Ende, M. E., Hoepelman, I. M., van Kasteren, M., Juttmann, J., Kuipers, M., Langebeek, N., Richter, C., Santegoets, R. M. W. J., Schrijnders-Gudde, L., van de Ven, B. J. M., Ormaasen, V., Aavitsland, P., Stanczak, J. J., Stanczak, G. P., Firlag-Burkacka, E., Wiercinska-Drapalo, A., Jablonowska, E., Malolepsza, E., Leszczyszyn-Pynka, M., Szata, W., Palma, C., Borges, F., Paix̃ao, T., Duque, V., Araújo, F., Jevtovic, D. J., Salemovic, D., Habekova, M., Mokráš, Miloš, Truska, P., Babic, Dunja Z., Tomazic, J., Vidmar, L., Karner, P., Gutíerrez, C., deMendoza, C., Erkicia, I., Domingo, P., Camino, X., Galindo, M. J., Blanco, J. L., Leal, M., Masabeu, A., Guelar, A., Llibre, J. M., Margall, N., Iribarren, J. A., Gutierrez, S., Baldov́i, J. F., Pedreira, J. D., Gatell, J. M., Moreno, S., de Mendoza, C., Soriano, V., Blaxhult, A., Heidarian, A., Karlsson, A., Aperia-Peipke, K., Bergbrant, I. -M, Gissĺen, M., Svennerholm, M., Björkman, Per, Bratt, G., Carlsson, M., Ekvall, H., Ericsson, M., Ḧofer, M., Johansson, B., Sonnerb̈org, A., Kuylenstierna, N., Ljungberg, B., Mäkitalo, S., Strand, A., Öberg, S., Virology, Erasmus MC other, Van Wijngaerden, Eric, Clinicum, Department of Medicine, Infektiosairauksien yksikkö, Centro de Malária e outras Doenças Tropicais (CMDT), Graduate School, Kostrikis, Leontios G. [0000-0002-5340-7109], Paraskevis, Dimitrios [0000-0001-6167-7152], UCL - SSS/IREC/MBLG - Pôle de Microbiologie médicale, UCL - (SLuc) Service de microbiologie, UCL - (SLuc) Service de médecine interne générale, Theys, K, Deforche, K, Vercauteren, J, Libin, P, van de Vijver, DA, Albert, J, Asjö, B, Balotta, C, Bruckova, M, Camacho, RJ, Clotet, B, Coughlan, S, Grossman, Z, Hamouda, O, Horban, A, Korn, K, Kostrikis, LG, Kücherer, C, Nielsen, C, Paraskevis, D, Poljak, M, Puchhammer Stockl, E, Riva, C, Ruiz, L, Liitsola, K, Schmit, JC, Schuurman, R, Sönnerborg, A, Stanekova, D, Stanojevic, M, Struck, D, Van Laethem, K, Wensing, AM, Boucher, CA, Vandamme, AM, Tramuto, F, and Vitale, F

Subjects
Adult, Male, lcsh:Immunologic diseases. Allergy, Anti-HIV Agents, education, Virulence, HIV Infections, Drug resistance, Biology, Settore MED/42 - Igiene Generale E Applicata, Virus, polymorphism, 03 medical and health sciences, Viral Proteins, SDG 3 - Good Health and Well-being, Virology, Genotype, Drug Resistance, Viral, drug-naive, medicine, Humans, Prospective Studies, 030304 developmental biology, 0303 health sciences, Polymorphism, Genetic, 030306 microbiology, Research, protease, Viral Load, Reverse transcriptase, 3. Good health, CD4 Lymphocyte Count, Drug-naïve, Infectious Diseases, 3121 General medicine, internal medicine and other clinical medicine, Immunology, biology.protein, HIV-1, Female, Antibody, lcsh:RC581-607, Viral load, HIV-1 infected patient, medicine.drug, Peptide Hydrolases
Abstract

Background: The effect of drug resistance transmission on disease progression in the newly infected patient is not well understood. Major drug resistance mutations severely impair viral fitness in a drug free environment, and therefore expected to revert quickly. Compensatory mutations, often already polymorphic in wild-type viruses, do not tend to revert after transmission. While compensatory mutations increase fitness during treatment, their presence may also modulate viral fitness and virulence in absence of therapy and major resistance mutations. We previously designed a modeling technique that quantifies genotypic footprints of in vivo treatment selective pressure, including both drug resistance mutations and polymorphic compensatory mutations, through the quantitative description of a fitness landscape from virus genetic sequences. Results: Genotypic correlates of viral load and CD4 cell count were evaluated in subtype B sequences from recently diagnosed treatment-naive patients enrolled in the SPREAD programme. The association of surveillance drug resistance mutations, reported compensatory mutations and fitness estimated from drug selective pressure fitness landscapes with baseline viral load and CD4 cell count was evaluated using regression techniques. Protease genotypic variability estimated to increase fitness during treatment was associated with higher viral load and lower CD4 cell counts also in treatment-naive patients, which could primarily be attributed to well-known compensatory mutations at highly polymorphic positions. By contrast, treatment-related mutations in reverse transcriptase could not explain viral load or CD4 cell count variability. Conclusions: These results suggest that polymorphic compensatory mutations in protease, reported to be selected during treatment, may improve the replicative capacity of HIV-1 even in absence of drug selective pressure or major resistance mutations. The presence of this polymorphic variation may either reflect a history of drug selective pressure, i.e. transmission from a treated patient, or merely be a result of diversity in wild-type virus. Our findings suggest that transmitted drug resistance has the potential to contribute to faster disease progression in the newly infected host and to shape the HIV-1 epidemic at a population level. ispartof: Retrovirology vol:9 issue:1 ispartof: location:England status: published

Published
2012

49. A note on uniqueness in the identification of a spacewise dependent source and diffusion coefficient for the heat equation

Author

De Cezaro, Adriano and Johansson, B. Tomas

Subjects
Mathematics - Analysis of PDEs, 35R30, 35A02, 65M32, 65L09, 74F05, 35K05, FOS: Mathematics, Mathematics - Numerical Analysis, Numerical Analysis (math.NA), Analysis of PDEs (math.AP)
Abstract

We investigate uniqueness in the inverse problem of reconstructing simultaneously a spacewise conductivity function and a heat source in the parabolic heat equation from the usual conditions of the direct problem and additional information from a supplementary temperature measurement at a given single instant of time. In the multi-dimensional case, we use Carleman estimates for parabolic equations to obtain a uniqueness result. The given data and the solution domain are sufficiently smooth such that the required norms and the derivatives of the conductivity, the source and the solution of the parabolic heat equation exist and are continuous throughout the solution domain. These assumptions can be further relaxed using more involved estimates and techniques but these lengthy details are not included. Instead, in the special case of the one-dimensional heat equation, we give an alternative and rather straightforward proof of uniqueness of the inverse problem, based on integral representations of the solution together with density results for solutions of the corresponding adjoint problem. In this case, the required regularity conditions on the conductivity, source and the solution of the parabolic heat equation are weakened to classes of integrable functions. Keywords: uniqueness; spacewise conductivity and source; final time measurements; heat equation; Carleman estimates., Comment: Submitted in October of 2012

Published
2012
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50. The method of fundamental solutions for the identification of a sound-soft obstacle in inverse acoustic scattering

Author

Karageorghis, Andreas, Johansson, B. T., Lesnic, D., and Karageorghis, Andreas [0000-0002-8399-6880]

Subjects
Inverse problems, Regularized meshless method, Acoustics, Inverse, Stable numerical solutions, Mesh-less methods, Mathematical techniques, Computational methods, Method of fundamental solutions, Far-field patterns, Acoustic scattering, Physics, Numerical Analysis, Scattered waves, Scattering, Applied Mathematics, Inverse problem, Computational Mathematics, Nonlinear system, Noise, Sound-soft obstacle, Inverse scattering problem, Numerical results, Homogeneous medium
Abstract

In this paper we propose a simple meshless method of fundamental solutions (MFS) for detecting a sound-soft scatterer embedded in a host acoustic homogeneous medium from the measurement of the far-field pattern of the scattered wave for only one incoming direction. Further, when this measurement is contaminated with noise, we augment the MFS with a nonlinear constrained regularized minimization for obtaining a stable numerical solution of the inverse problem. Numerical results are presented and discussed. © 2012 IMACS. 62 12 1767 1780 Cited By :4

Published
2012

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