| 1. |
- Galván, Ignacio Fdez., et al.
(författare)
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OpenMolcas : From Source Code to Insight
- 2019
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 15:11, s. 5925-5964
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Tidskriftsartikel (refereegranskat)abstract
- In this Article we describe the OpenMolcas environment and invite the computational chemistry community to collaborate. The open-source project already includes a large number of new developments realized during the transition from the commercial MOLCAS product to the open-source platform. The paper initially describes the technical details of the new software development platform. This is followed by brief presentations of many new methods, implementations, and features of the OpenMolcas program suite. These developments include novel wave function methods such as stochastic complete active space self-consistent field, density matrix renormalization group (DMRG) methods, and hybrid multiconfigurational wave function and density functional theory models. Some of these implementations include an array of additional options and functionalities. The paper proceeds and describes developments related to explorations of potential energy surfaces. Here we present methods for the optimization of conical intersections, the simulation of adiabatic and nonadiabatic molecular dynamics, and interfaces to tools for semiclassical and quantum mechanical nuclear dynamics. Furthermore, the Article describes features unique to simulations of spectroscopic and magnetic phenomena such as the exact semiclassical description of the interaction between light and matter, various X-ray processes, magnetic circular dichroism, and properties. Finally, the paper describes a number of built-in and add-on features to support the OpenMolcas platform with postcalculation analysis and visualization, a multiscale simulation option using frozen-density embedding theory, and new electronic and muonic basis sets.
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| 2. |
- Locke, Adam E, et al.
(författare)
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Genetic studies of body mass index yield new insights for obesity biology.
- 2015
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 518:7538, s. 197-401
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Tidskriftsartikel (refereegranskat)abstract
- Obesity is heritable and predisposes to many diseases. To understand the genetic basis of obesity better, here we conduct a genome-wide association study and Metabochip meta-analysis of body mass index (BMI), a measure commonly used to define obesity and assess adiposity, in up to 339,224 individuals. This analysis identifies 97 BMI-associated loci (P < 5 × 10(-8)), 56 of which are novel. Five loci demonstrate clear evidence of several independent association signals, and many loci have significant effects on other metabolic phenotypes. The 97 loci account for ∼2.7% of BMI variation, and genome-wide estimates suggest that common variation accounts for >20% of BMI variation. Pathway analyses provide strong support for a role of the central nervous system in obesity susceptibility and implicate new genes and pathways, including those related to synaptic function, glutamate signalling, insulin secretion/action, energy metabolism, lipid biology and adipogenesis.
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| 3. |
- Tahmasebi, Nina, 1982, et al.
(författare)
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Visions and open challenges for a knowledge-based culturomics
- 2015
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Ingår i: International Journal on Digital Libraries. - : Springer Science and Business Media LLC. - 1432-5012 .- 1432-1300. ; 15:2-4, s. 169-187
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Tidskriftsartikel (refereegranskat)abstract
- The concept of culturomics was born out of the availability of massive amounts of textual data and the interest to make sense of cultural and language phenomena over time. Thus far however, culturomics has only made use of, and shown the great potential of, statistical methods. In this paper, we present a vision for a knowledge-based culturomics that complements traditional culturomics. We discuss the possibilities and challenges of combining knowledge-based methods with statistical methods and address major challenges that arise due to the nature of the data; diversity of sources, changes in language over time as well as temporal dynamics of information in general. We address all layers needed for knowledge-based culturomics, from natural language processing and relations to summaries and opinions.
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| 4. |
- Adesam, Yvonne, 1975, et al.
(författare)
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The Eukalyptus Treebank of Written Swedish
- 2018
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Ingår i: Seventh Swedish Language Technology Conference (SLTC), Stockholm, 7–9 November 2018.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 5. |
- Aggestam, Lisbeth, 1965, et al.
(författare)
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Leadership roles and institutional change in EU foreign policy
- 2017
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Ingår i: Paper prepared for the 24th International Conference of Europeanists, Council for European Studies (CES). University of Glasgow: 12-14 July.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Can you have a strategy without leadership? The question is an urgent one for the European Union (EU) that is currently experiencing one of its severest crisis. Leadership is often seen as a necessary condition for establishing a shared vision and common action that the EU Global Strategy calls for. But who can provide leadership in EU foreign and security policy and how? This question relates to the broader literature that study when and how executives of international organizations possess agency to exercise leadership and to what affect. In this paper, we focus on the double-hatted position that the EU High Representative for foreign affairs and security policy (HR) has alongside her role as Vice-President of the European Commission. The latest treaty reforms of the EU brought about significant institutional changes that strengthened the formal position of the HR. These developments in EU foreign policy-making have confounded scholars of European integration who disagree on their significance. One strand of research points to the symbolic challenge that these formal shifts in the leadership function represents to state-centric ideas about foreign policy and diplomacy. Others have argued that these changes do not represent such a substantive shift in the principal-agent relationship as the intergovernmental nature of decision-making has been essentially preserved. Whereas the former view would imply possibilities for new political leadership in EU foreign policy, the latter strand would rather see these institutional developments as providing for a more managerial role. This paper examines these two distinct trajectories of European integration that entails different types of leadership roles taken by the EU High Representative. We are particularly interested in exploring the horizontal dimension of the double-hatted position that the HR finds herself in as Head of the hybrid institution of the EEAS and that of Vice-President of the supranational European Commission. While the first post-Lisbon HR, Catherine Ashton, had her headquarter in the EEAS, the second HR Federica Moghereni, appointed in 2014, has moved her office to the Commission. We ask in this paper what is the effect of this institutional change for the role of the HR, and the expectations on her leadership. The paper is based on an empirical survey that includes 125 respondents from EU member states and EU institutions in order to explore the extent to which the HR and EEAS is perceived to take on a political leadership role or a more managerial role.
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| 6. |
- Aggestam, Lisbeth, 1965, et al.
(författare)
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Mapping leadership roles in EU foreign policy
- 2016
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Ingår i: 8th Pan-European Conference on the European Union (ECPR). Trento, Italy: 15-18 June.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- This paper examines the nature of leadership in EU foreign policy. The latest treaty reforms of the European Union involve a significant institutional delegation and centralisation to Brussels of the formal leadership functions in the field of foreign policy. This is puzzling given that theories of European integration discount that a significant delegation of leadership will happen in the high politics of foreign policy given its close association to sovereignty and statehood. In this paper, we set out to explore a paradox at the heart of EU foreign policy between the demand for leadership effectiveness (strategic action) and perceptions of legitimate leadership (appropriate behaviour). We suggest that the analysis of leadership in EU foreign policy is dependent on how we regard institutions, and propose that social role theory can provide an original analytical perspective from which to study the contested nature of leadership in EU foreign policy. We argue that not only formal institutions determine leadership in EU foreign policy, but that the enactment of leadership is crucially shaped by the possibilities for role relations (a shared organizational reality) between leaders and followers. Based on survey data, this paper explores what leadership role expectations representatives of EU member states and European External Action Service (EEAS) officials have. The empirical findings indicate that there are diverging perceptions about the post-Lisbon leadership functions in EU foreign policy, and that member states still have a leadership role to play. We also show that the perceptions about leadership performance differ between member states and EEAS officials, and that there are constraints to the independent agency held by the EU High Representative.
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| 7. |
- Aggestam, Lisbeth, 1965, et al.
(författare)
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The Leadership Paradox in EU Foreign Policy
- 2017
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Ingår i: Journal of Common Market Studies. - : Wiley. - 0021-9886 .- 1468-5965.
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Tidskriftsartikel (refereegranskat)abstract
- This article examines a leadership paradox at the heart of EU foreign policy between the demand for effective European leadership, and leadership legitimacy embedded in state practices. This paradox is manifested in the Lisbon treaty that delegated significant formal leadership functions to the European level. We probe the question how and by whom leadership can and should be performed in EU foreign policy. To answer this question, we advance a new theoretical framework drawing on sociological institutionalism and role theory. We argue that leadership should be understood as a social role shaped in a process of interaction between leader and followers. We contribute with new empirical knowledge of leadership role relations based on an interview survey conducted in 2016. The empirical results point to role conflicts over the formal leadership functions in EU foreign policy and the emergence of new informal leadership practices by EU member states.
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| 8. |
- Ahlen, Anders, et al.
(författare)
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Toward Wireless Control in Industrial Process Automation : A Case Study at a Paper Mill
- 2019
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Ingår i: IEEE Control Systems. - : Institute of Electrical and Electronics Engineers (IEEE). - 1066-033X .- 1941-000X. ; 39:5, s. 36-57
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Tidskriftsartikel (refereegranskat)abstract
- Wireless sensors and networks are used only occasionally in current control loops in the process industry. With rapid developments in embedded and highperformance computing, wireless communication, and cloud technology, drastic changes in the architecture and operation of industrial automation systems seem more likely than ever. These changes are driven by ever-growing demands on production quality and flexibility. However, as discussed in "Summary," there are several research obstacles to overcome. The radio communication environment in the process industry is often troublesome, as the environment is frequently cluttered with large metal objects, moving machines and vehicles, and processes emitting radio disturbances [1], [2]. The successful deployment of a wireless control system in such an environment requires careful design of communication links and network protocols as well as robust and reconfigurable control algorithms.
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| 9. |
- Ahlén, Anders, et al.
(författare)
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Towards Wireless Control in Industrial Process Automation : A Case Study at a Paper Mill
- 2019
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Ingår i: IEEE CONTROL SYSTEMS MAGAZINE. - : IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC. - 1066-033X .- 1941-000X. ; 39:5, s. 36-57
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Tidskriftsartikel (refereegranskat)abstract
- Wireless sensors and networks are used only occasionally in current control loops in the process industry. With rapid developments in embedded and highperformance computing, wireless communication, and cloud technology, drastic changes in the architecture and operation of industrial automation systems seem more likely than ever. These changes are driven by ever-growing demands on production quality and flexibility. However, as discussed in "Summary," there are several research obstacles to overcome. The radio communication environment in the process industry is often troublesome, as the environment is frequently cluttered with large metal objects, moving machines and vehicles, and processes emitting radio disturbances [1], [2]. The successful deployment of a wireless control system in such an environment requires careful design of communication links and network protocols as well as robust and reconfigurable control algorithms.
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| 10. |
- Ahlén Bergman, Emma, et al.
(författare)
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Increased CD4+ T cell lineage commitment determined by CpG methylation correlates with better prognosis in urinary bladder cancer patients
- 2018
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Ingår i: Clinical Epigenetics. - : BMC. - 1868-7083 .- 1868-7075. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Urinary bladder cancer is a common malignancy worldwide. Environmental factors and chronic inflammation are correlated with the disease risk. Diagnosis is performed by transurethral resection of the bladder, and patients with muscle invasive disease preferably proceed to radical cystectomy, with or without neoadjuvant chemotherapy. The anti-tumour immune responses, known to be initiated in the tumour and draining lymph nodes, may play a major role in future treatment strategies. Thus, increasing the knowledge of tumour-associated immunological processes is important. Activated CD4+ T cells differentiate into four main separate lineages: Th1, Th2, Th17 and Treg, and they are recognized by their effector molecules IFN-γ, IL-13, IL-17A, and the transcription factor Foxp3, respectively. We have previously demonstrated signature CpG sites predictive for lineage commitment of these four major CD4+ T cell lineages. Here, we investigate the lineage commitment specifically in tumour, lymph nodes and blood and relate them to the disease stage and response to neoadjuvant chemotherapy.RESULTS: Blood, tumour and regional lymph nodes were obtained from patients at time of transurethral resection of the bladder and at radical cystectomy. Tumour-infiltrating CD4+ lymphocytes were significantly hypomethylated in all four investigated lineage loci compared to CD4+ lymphocytes in lymph nodes and blood (lymph nodes vs tumour-infiltrating lymphocytes: IFNG -4229 bp p < 0.0001, IL13 -11 bp p < 0.05, IL17A -122 bp p < 0.01 and FOXP3 -77 bp p > 0.05). Examination of individual lymph nodes displayed different methylation signatures, suggesting possible correlation with future survival. More advanced post-cystectomy tumour stages correlated significantly with increased methylation at the IFNG -4229 bp locus. Patients with complete response to neoadjuvant chemotherapy displayed significant hypomethylation in CD4+ T cells for all four investigated loci, most prominently in IFNG p < 0.0001. Neoadjuvant chemotherapy seemed to result in a relocation of Th1-committed CD4+ T cells from blood, presumably to the tumour, indicated by shifts in the methylation patterns, whereas no such shifts were seen for lineages corresponding to IL13, IL17A and FOXP3.CONCLUSION: Increased lineage commitment in CD4+ T cells, as determined by demethylation in predictive CpG sites, is associated with lower post-cystectomy tumour stage, complete response to neoadjuvant chemotherapy and overall better outcome, suggesting epigenetic profiling of CD4+ T cell lineages as a useful readout for clinical staging.
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