| 1. |
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| 2. |
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| 3. |
- Christerson, Linus, et al.
(author)
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Typing of Lymphogranuloma Venereum Chlamydia trachomatis Strains
- 2010
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In: Emerging Infectious Diseases. - : Centers for Disease Control and Prevention (CDC). - 1080-6040 .- 1080-6059. ; 16:11, s. 1777-1779
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Journal article (peer-reviewed)abstract
- We analyzed by multilocus sequence typing 77 lymphogranuloma venereum Chlamydia trachomatis strains from men who have sex with men in Europe and the United States. Specimens from an outbreak in 2003 in Europe were monoclonal. In contrast, several strains were in the United States in the 1980s, including a variant from Europe.
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| 4. |
- Donahue, N. M., et al.
(author)
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Aging of biogenic secondary organic aerosol via gas-phase OH radical reactions
- 2012
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In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 109:34, s. 13503-13508
-
Journal article (peer-reviewed)abstract
- The Multiple Chamber Aerosol Chemical Aging Study (MUCHACHAS) tested the hypothesis that hydroxyl radical (OH) aging significantly increases the concentration of first-generation biogenic secondary organic aerosol (SOA). OH is the dominant atmospheric oxidant, and MUCHACHAS employed environmental chambers of very different designs, using multiple OH sources to explore a range of chemical conditions and potential sources of systematic error. We isolated the effect of OH aging, confirming our hypothesis while observing corresponding changes in SOA properties. The mass increases are consistent with an existing gap between global SOA sources and those predicted in models, and can be described by a mechanism suitable for implementation in those models.
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| 5. |
- Filieri, Antonio, et al.
(author)
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Automated Design of Self-Adaptive Software with Control-Theoretical Formal Guarantees
- 2014
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Conference paper (peer-reviewed)abstract
- Self-adaptation enables software to execute successfully in dynamic, unpredictable, and uncertain environments. Control theory provides a broad set of mathematically grounded techniques for adapting the behavior of dynamic systems. While it has been applied to specific software control problems, it has proved difficult to define methodologies allowing non-experts to systematically apply control techniques to create adaptive software. These difficulties arise because computer systems are usually non-linear, with varying workloads and heterogeneous components, making it difficult to model software as a dynamic system; i.e., by means of differential or difference equations. This paper proposes a broad scope methodology for automatically constructing both an approximate dynamic model of a software system and a suitable controller for managing its non-functional requirements. Despite its generality, this methodology provides formal guarantees concerning the system's dynamic behavior by keeping its model continuously updated to compensate for changes in the execution environment and effects of the initial approximation. We apply the methodology to three case studies, demonstrating its generality by tackling different domains (and different non-functional requirements) with the same approach. Being broadly applicable and fully automated, this methodology may allow the adoption of control theoretical solutions (and their formal properties) for a wide range of software adaptation problems.
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| 6. |
- Hoffmann, Henry, et al.
(author)
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A generalized software framework for accurate and efficient management of performance goals
- 2013
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In: 2013 Proceedings of the International Conference on Embedded Software, EMSOFT 2013. - 9781479914432
-
Conference paper (peer-reviewed)abstract
- A number of techniques have been proposed to provide runtime performance guarantees while minimizing power consumption. One drawback of existing approaches is that they work only on a fixed set of components (or actuators) that must be specified at design time. If new components become available, these management systems must be redesigned and reimplemented. In this paper, we propose PTRADE, a novel performance management framework that is general with respect to the components it manages. PTRADE can be deployed to work on a new system with different components without redesign and reimplementation. PTRADE's generality is demonstrated through the management of performance goals for a variety of benchmarks on two different Linux/x86 systems and a simulated 128-core system, each with different components governing power and performance tradeoffs. Our experimental results show that PTRADE provides generality while meeting performance goals with low error and close to optimal power consumption.
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| 7. |
- Hoffmann, Henry, et al.
(author)
-
A Generalized Software System for Accurate and Efficient Management of Application Performance Goals
- 2013
-
Conference paper (peer-reviewed)abstract
- A number of techniques have been proposed to provide run- time performance guarantees while minimizing power consumption. One drawback of existing approaches is that they work only on a fixed set of components (or actuators) that must be specified at design time. If new components become available, these management systems must be redesigned and reimplemented. In this paper, we propose PTRADE, a novel performance management framework that is general with respect to the components it manages. PTRADE can be deployed to work on a new system with different components without redesign and reimplementation. PTRADE’s generality is demonstrated through the management of performance goals for a variety of benchmarks on two different Linux/x86 systems and a simulated 128-core system, each with different components governing power and performance tradeoffs. Our experimental results show that PTRADE provides generality while meeting performance goals and ap- proaching optimal power consumption. PTRADE consumes only 7% more power than optimal on the Linux/x86 systems and 3% more power than optimal on the simulated many-core.
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| 8. |
- Hoffmann, Henry, et al.
(author)
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PCP: A Generalized Approach to Optimizing Performance Under Power Constraints through Resource Management
- 2014
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Conference paper (peer-reviewed)abstract
- Many computing systems are constrained by power budgets. While they could temporarily draw more power, doing so creates unsustainable temperatures and unwanted electricity consumption. Developing systems that operate within power budgets is a constrained optimization problem: configuring the components within the system to maximize performance while maintaining sustainable power consumption. This is a challenging problem because many different components within a system affect power/performance tradeoffs and they interact in complex ways. Prior approaches address these challenges by fixing a set of components and designing a power budgeting framework that manages only that one set of components. If new components become available, then this framework must be redesigned and reimplemented. This paper presents PCP, a general solution to the power budgeting problem that works with arbitrary sets of components, even if they are not known at design time or change during runtime. To demonstrate PCP we implement it in software and deploy it on a Linux/x86 platform.
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| 9. |
- Hoffmann, Henry, et al.
(author)
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Self-aware computing in the Angstrom processor
- 2012
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In: Proceedings of the 49th Annual Design Automation Conference. - New York, NY, USA : ACM. - 9781450311991 ; , s. 259-264
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Conference paper (peer-reviewed)abstract
- Addressing the challenges of extreme scale computing re- quires holistic design of new programming models and sys- tems that support those models. This paper discusses the Angstrom processor, which is designed to support a new Self-aware Computing (SEEC) model. In SEEC, applications explicitly state goals, while other systems components provide actions that the SEEC runtime system can use to meet those goals. Angstrom supports this model by ex- posing sensors and adaptations that traditionally would be managed independently by hardware. This exposure allows SEEC to coordinate hardware actions with actions specified by other parts of the system, and allows the SEEC runtime system to meet application goals while reducing costs (e.g., power consumption).
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| 10. |
- Laettig-Tuennemann, Gisela, et al.
(author)
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Backbone rigidity and static presentation of guanidinium groups increases cellular uptake of arginine-rich cell-penetrating peptides
- 2011
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 2, s. 453-
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Journal article (peer-reviewed)abstract
- In addition to endocytosis-mediated cellular uptake, hydrophilic cell-penetrating peptides are able to traverse biological membranes in a non-endocytic mode termed transduction, resulting in immediate bioavailability. Here we analysed structural requirements for the non-endocytic uptake mode of arginine-rich cell-penetrating peptides, by a combination of live-cell microscopy, molecular dynamics simulations and analytical ultracentrifugation. We demonstrate that the transduction efficiency of arginine-rich peptides increases with higher peptide structural rigidity. Consequently, cyclic arginine-rich cell-penetrating peptides showed enhanced cellular uptake kinetics relative to their linear and more flexible counterpart. We propose that guanidinium groups are forced into maximally distant positions by cyclization. This orientation increases membrane contacts leading to enhanced cell penetration.
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| 11. |
- Maggio, Martina, et al.
(author)
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ARPE : A tool to build equation models of computing systems
- 2013
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Conference paper (peer-reviewed)abstract
- An important challenge in the design and implementation of self-optimizing systems is that of finding a model that maps changes in a tunable parameter (or “knob”) into an effect on the performance, power, or energy, of the overall system. This paper describes ARPE (Analyzing the Relationship between Parameters and Effectors), an open source tool to analyze the effect of parameter changes on the behavior of applications in a complex system with interrelated knobs. We evaluate ARPE in several case studies on real systems with different sensors and parameters. Our results show that ARPE can help determine the best sensors for a system designed to predict application execution time. For space limitations, only one case study is here shown, demonstrating that the error of modeling energy consumption is limited to the range 0.1−10% for previously unseen benchmarks.
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| 12. |
- Maggio, Martina, et al.
(author)
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Comparison of Decision Making Strategies for Self-Optimization in Autonomic Computing Systems
- 2012
-
In: ACM Transactions on Autonomous and Adaptive Systems. - : Association for Computing Machinery (ACM). - 1556-4665 .- 1556-4703. ; 7:4
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Journal article (peer-reviewed)abstract
- Autonomic computing systems are capable of adapting their behavior and resources thousands of times a second to automatically decide the best way to accomplish a given goal despite changing environmental conditions and demands. Different decision mechanisms are considered in the literature, but in the vast majority of the cases a single technique is applied to a given instance of the problem. This paper proposes a comparison of some state of the art approaches for decision making, applied to a self-optimizing autonomic system that allocates resources to a software application. A variety of decision mechanisms, from heuristics to control-theory and machine learning, are investigated. The results obtained with these solutions are compared by means of case studies using standard benchmarks. Our results indicate that the most suitable decision mechanism can vary depending on the specific test case but adaptive and model predictive control systems tend to produce good performance and may work best in a priori unknown situations.
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| 13. |
- Maggio, Martina, et al.
(author)
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Power Optimization in Embedded Systems via Feedback Control of Resource Allocation
- 2013
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In: IEEE Transactions on Control Systems Technology. - 1558-0865. ; 21:1, s. 239-246
-
Journal article (peer-reviewed)abstract
- Embedded systems often operate in so variable con- ditions that design can only be carried out for some worst-case scenario. This leads to over-provisioned resources, and undue power consumption. Feedback control is an effective (and not yet fully explored) way to tailor resource usage online, thereby making the system behave and consume as if it was optimized for each specific utilization case. A control-theoretical methodology is here proposed to complement architecture design in a view to said tailoring. Experimental results show that a so addressed architecture meets performance requirements, while consuming less power than any fixed (i.e., uncontrolled) one capable of attaining the same goals. Also, the methodology naturally induces computationally lightweight control laws.
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| 14. |
- O'Seaghdha, Conall M., et al.
(author)
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Meta-Analysis of Genome-Wide Association Studies Identifies Six New Loci for Serum Calcium Concentrations
- 2013
-
In: PLOS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 9:9, s. e1003796-
-
Journal article (peer-reviewed)abstract
- Calcium is vital to the normal functioning of multiple organ systems and its serum concentration is tightly regulated. Apart from CASR, the genes associated with serum calcium are largely unknown. We conducted a genome-wide association meta-analysis of 39,400 individuals from 17 population-based cohorts and investigated the 14 most strongly associated loci in <= 21,679 additional individuals. Seven loci (six new regions) in association with serum calcium were identified and replicated. Rs1570669 near CYP24A1 (P = 9.1E-12), rs10491003 upstream of GATA3 (P = 4.8E-09) and rs7481584 in CARS (P = 1.2E-10) implicate regions involved in Mendelian calcemic disorders: Rs1550532 in DGKD (P = 8.2E-11), also associated with bone density, and rs7336933 near DGKH/KIAA0564 (P = 9.1E-10) are near genes that encode distinct isoforms of diacylglycerol kinase. Rs780094 is in GCKR. We characterized the expression of these genes in gut, kidney, and bone, and demonstrate modulation of gene expression in bone in response to dietary calcium in mice. Our results shed new light on the genetics of calcium homeostasis.
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| 15. |
- Aad, G., et al.
(author)
-
- 2011
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swepub:Mat__t (peer-reviewed)
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| 16. |
- Aad, G., et al.
(author)
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- 2011
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Journal article (peer-reviewed)
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| 17. |
- Aad, G., et al.
(author)
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- 2012
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swepub:Mat__t (peer-reviewed)
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| 18. |
- Aad, G., et al.
(author)
-
- 2012
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swepub:Mat__t (peer-reviewed)
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| 19. |
- Aad, G., et al.
(author)
-
- 2011
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swepub:Mat__t (peer-reviewed)
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| 20. |
- Aad, G., et al.
(author)
-
- 2013
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swepub:Mat__t (peer-reviewed)
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| 21. |
- Aad, G., et al.
(author)
-
- 2012
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swepub:Mat__t (peer-reviewed)
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| 22. |
- Aad, G., et al.
(author)
-
- 2012
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swepub:Mat__t (peer-reviewed)
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| 23. |
- Aad, G., et al.
(author)
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- 2012
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swepub:Mat__t (peer-reviewed)
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| 24. |
- Aad, G., et al.
(author)
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- 2012
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swepub:Mat__t (peer-reviewed)
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| 25. |
- Aad, G., et al.
(author)
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- 2012
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swepub:Mat__t (peer-reviewed)
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| 26. |
- Aad, G., et al.
(author)
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- 2012
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swepub:Mat__t (peer-reviewed)
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| 27. |
- Aad, G., et al.
(author)
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- 2012
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swepub:Mat__t (peer-reviewed)
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| 28. |
- Aad, G., et al.
(author)
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- 2012
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swepub:Mat__t (peer-reviewed)
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| 29. |
- Aad, G., et al.
(author)
-
- 2012
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swepub:Mat__t (peer-reviewed)
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| 30. |
- Aad, G., et al.
(author)
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- 2012
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swepub:Mat__t (peer-reviewed)
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| 31. |
- Aad, G., et al.
(author)
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- 2011
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swepub:Mat__t (peer-reviewed)
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| 32. |
- Aad, G., et al.
(author)
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- 2011
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swepub:Mat__t (peer-reviewed)
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| 33. |
- Aad, G., et al.
(author)
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- 2011
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swepub:Mat__t (peer-reviewed)
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| 34. |
- Aad, G., et al.
(author)
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- 2011
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swepub:Mat__t (peer-reviewed)
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| 35. |
- Aad, G., et al.
(author)
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- 2012
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swepub:Mat__t (peer-reviewed)
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| 36. |
- Aad, G., et al.
(author)
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- 2012
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Journal article (peer-reviewed)
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| 37. |
- Aad, G., et al.
(author)
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- 2012
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swepub:Mat__t (peer-reviewed)
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| 38. |
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(author)
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- 2012
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swepub:Mat__t (peer-reviewed)
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| 39. |
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(author)
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- 2013
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swepub:Mat__t (peer-reviewed)
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| 40. |
- Aad, G., et al.
(author)
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- 2012
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Journal article (peer-reviewed)
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| 41. |
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(author)
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- 2012
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| 42. |
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swepub:Mat__t (peer-reviewed)
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| 44. |
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swepub:Mat__t (peer-reviewed)
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| 45. |
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(author)
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- 2011
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swepub:Mat__t (peer-reviewed)
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| 46. |
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- 2012
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| 47. |
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- 2011
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swepub:Mat__t (peer-reviewed)
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