| 1. |
- Menkveld, Albert J., et al.
(författare)
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Nonstandard Errors
- 2024
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Ingår i: JOURNAL OF FINANCE. - : Wiley-Blackwell. - 0022-1082 .- 1540-6261. ; 79:3, s. 2339-2390
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Tidskriftsartikel (refereegranskat)abstract
- In statistics, samples are drawn from a population in a data-generating process (DGP). Standard errors measure the uncertainty in estimates of population parameters. In science, evidence is generated to test hypotheses in an evidence-generating process (EGP). We claim that EGP variation across researchers adds uncertainty-nonstandard errors (NSEs). We study NSEs by letting 164 teams test the same hypotheses on the same data. NSEs turn out to be sizable, but smaller for more reproducible or higher rated research. Adding peer-review stages reduces NSEs. We further find that this type of uncertainty is underestimated by participants.
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| 2. |
- Moore, Keith J M, et al.
(författare)
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Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications
- 2021
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Ingår i: Journal of Biomolecular Techniques. - : Association of Biomolecular Resource Facilities. - 1524-0215 .- 1943-4731. ; 32:3, s. 228-275
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Forskningsöversikt (refereegranskat)abstract
- As the second year of the COVID-19 pandemic begins, it remains clear that a massive increase in the ability to test for SARS-CoV-2 infections in a myriad of settings is critical to controlling the pandemic and to preparing for future outbreaks. The current gold standard for molecular diagnostics is the polymerase chain reaction (PCR), but the extraordinary and unmet demand for testing in a variety of environments means that both complementary and supplementary testing solutions are still needed. This review highlights the role that loop-mediated isothermal amplification (LAMP) has had in filling this global testing need, providing a faster and easier means of testing, and what it can do for future applications, pathogens, and the preparation for future outbreaks. This review describes the current state of the art for research of LAMP-based SARS-CoV-2 testing, as well as its implications for other pathogens and testing. The authors represent the global LAMP (gLAMP) Consortium, an international research collective, which has regularly met to share their experiences on LAMP deployment and best practices; sections are devoted to all aspects of LAMP testing, including preanalytic sample processing, target amplification, and amplicon detection, then the hardware and software required for deployment are discussed, and finally, a summary of the current regulatory landscape is provided. Included as well are a series of first-person accounts of LAMP method development and deployment. The final discussion section provides the reader with a distillation of the most validated testing methods and their paths to implementation. This review also aims to provide practical information and insight for a range of audiences: for a research audience, to help accelerate research through sharing of best practices; for an implementation audience, to help get testing up and running quickly; and for a public health, clinical, and policy audience, to help convey the breadth of the effect that LAMP methods have to offer.
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| 3. |
- Lindgren, Per, et al.
(författare)
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A Real-Time Semantics for the IEC 61499 standard
- 2015
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Ingår i: Proceedings of 2015 IEEE 20th International Conference on Emerging Technologies & Factory Automation (ETFA 2015). - Piscataway, NJ : IEEE Communications Society. - 9781467379298
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Konferensbidrag (refereegranskat)abstract
- The IEC 61499 standard provides an executable model for distributed control systems in terms of interacting function blocks. However, the current IEC 61499 standard lacks appropriate timing semantics for the specification of timing requirements, reasoning on timing properties at the model level, and for the timing verification of a specific deployment. In this paper we address this fundamental shortcoming by proposing Real-Time-4-FUN, a real-time semantics for IEC 61499. The key property is the preservation of non-determinism, allowing us to reason on (and verify) timing properties at the model level without assuming any specific scheduling policy or stipulating specific order of execution for the deployment. This provides for a clear separation of concerns, where the designer can focus on properties of the application prior to, and separately from, deployment verification. The proposed timing semantics is backwards compatible to the current standard, thus allow for reuse of existing designs. The transitional property allows timing requirements to propagate to downstream sub-systems, and can be utilized for scheduling both at device and network level. Based on a translation to RTFM-tasks and resources, IEC 61499 the models can be analyzed, compiled and executed. As a proof of concept the timing semantics has been experimentally implemented in the RTFM-core language and the accompanying (thread based) RTFM-RT run-time system.
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| 4. |
- Lindgren, Per, et al.
(författare)
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Abstract Timers and their Implementation onto the ARM Cortex-M family of MCUs
- 2016
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Ingår i: SIGBED Review. - : Association for Computing Machinery (ACM). - 1551-3688. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Real-Time For the Masses (RTFM) is a set of languages andtools being developed to facilitate embedded software developmentand provide highly ecient implementations gearedto static verication. The RTFM-kernel is an architecturedesigned to provide highly ecient and predicable Stack ResourcePolicy based scheduling, targeting bare metal (singlecore)platforms.We contribute by introducing a platform independent timerabstraction that relies on existing RTFM-kernel primitives.We develop two alternative implementations for the ARMCortex-M family of MCUs: a generic implementation, usingthe ARM dened SysTick/DWT hardware; and a targetspecic implementation, using the match compare/free runningtimers. While sacricing generality, the latter is moreexible and may reduce overall overhead. Invariants for correctnessare presented, and methods to static and run-timeverication are discussed. Overhead is bound and characterized.In both cases the critical section from release timeto dispatch is less than 2us on a 100MHz MCU. Queue andtimer mechanisms are directly implemented in the RTFMcorelanguage (-core in the following) and can be includedin system-wide scheduling analysis.
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| 5. |
- Lindgren, Per, et al.
(författare)
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End-to-End Response Time of 61499 Distributed Applications over Switched Ethernet
- 2017
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Ingår i: IEEE Transactions on Industrial Informatics. - : IEEE. - 1551-3203 .- 1941-0050. ; 13:1, s. 287-297
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Tidskriftsartikel (refereegranskat)abstract
- The IEC 61499 standard provides means to specify distributed control systems in terms of function blocks. For the deployment, each device may hold one or many logical resources, each consisting of a function block network with service interface blocks at the edges. The execution model is event driven (asynchronous), where triggering events may be associated with data (and seen as messages). In this paper, we propose a low complexity implementation technique allowing to assess end-to-end response times of event chains spanning over a set of networked devices. Based on a translation of IEC 61499 to RTFM1-tasks and resources, the response time for each task in the system at device-level can be derived using established scheduling techniques. In this paper, we develop a holistic method to provide safe end-to-end response times taking both intra- and inter-device delivery delays into account. The novelty of our approach is the accuracy of the system scheduling overhead characterization. While the device-level (RTFM) scheduling overhead was discussed in previous works, the network-level scheduling overhead for switched Ethernets is discussed in this paper. The approach is generally applicable to a wide range of COTS Ethernet switches without a need for expensive custom solutions to provide hard real-time performance. A behavior characterization of the utilized switch determines the guaranteed response times. As a use case, we study the implementation onto (single-core) ARMcortex based devices communicating over a switched Ethernet network. For the analysis, we define a generic switch model and an experimental setup allowing us to study the impact of network topology as well as 802.1Q quality of service in a mixed critical setting. Our results indicate that safe sub millisecond end-to-end response times can be obtained using the proposed approach.
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| 6. |
- Lindgren, Per, et al.
(författare)
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Response Time for IEC 61499 over Ethernet
- 2015
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Ingår i: IEEE International Conference on Industrial Informatics. - Piscataway, NJ : IEEE Communications Society. - 9781479966493 ; , s. 1206-1212
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Konferensbidrag (refereegranskat)abstract
- The IEC 61499 standard provides means to specify distributed control systems in terms of function blocks. For the deployment, each device may hold one or many logical resources, each consisting of a function block network with service interface blocks at the edges. The execution model is event driven (asynchronous), where triggering events may be associated with data (and seen as a message). In this paper we propose a low complexity implementation technique allowing to asses end-to-end response time of event chains spanning a networked devices. Based on a translation of IEC 61499 to RTFM-tasks and resources, the response time for each task in the system can be derived using established scheduling techniques. In this paper we develop a method to provide safe end-to-end response time taking both intra- and inter-device delivery delays into account. As a use case we study the implementation onto (single-core) ARMcortex based devices communicating over a switched Ethernet network. For the analysis we define a generic switch model, and an experimental setup allowing us to study the impact of network topology as well as 802.1Q quality of service in a mixed critical setting. Our results indicate that safe sub milli-second end-to-end response times can be obtained using the proposed approach.
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| 7. |
- Lindgren, Per, et al.
(författare)
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RTFM-core : Language and Implementation
- 2015
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Ingår i: 2015 IEEE 10th Conference on Industrial Electronics and Applications (ICIEA). - Piscataway, NJ : IEEE Communications Society. - 9781479983896 ; , s. 990-995
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Konferensbidrag (refereegranskat)abstract
- Robustness, real-time properties and resource efficiency are key properties to embedded devices of the CPS/IoT era. In this paper we propose a language approach RTFMcore, and show its potential to facilitate the development process and provide highly efficient and statically verifiable implementations. Our programming model is reactive, based on the familiar notions of concurrent tasks and (single-unit) resources. The language is kept minimalistic, capturing the static task, communication and resource structure of the system. Whereas C-source can be arbitrarily embedded in the model, and/or externally referenced, the instep to mainstream development is minimal, and a smooth transition of legacy code is possible. A prototype compiler implementation for RTFM-core is presented. The compiler generates C-code output that compiled together withtheRTFM-kernelprimitivesrunsonbaremetal.TheRTFMkernel guarantees deadlock-lock free execution and efficiently exploits the underlying interrupt hardware for static priority scheduling and resource management under the Stack Resource Policy. This allows a plethora of well-known methods to static verification (response time analysis, stack memory analysis, etc.) to be readily applied. The proposed language and supporting tool-chain is demonstrated by showing the complete process from RTFM-core source code into bare metal executables for a lightweight ARM-Cortex M3 target.
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| 8. |
- Lindgren, Per, et al.
(författare)
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Well formed Control-flow for Critical Sections in RTFM-core
- 2015
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Ingår i: IEEE International Conference on Industrial Informatics. - Piscataway, NJ : IEEE Communications Society. - 9781479966493 ; , s. 1438-1445
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Konferensbidrag (refereegranskat)abstract
- The mainstream of embedded software development as of today is dominated by C programming. To aid the development, hardware abstractions, libraries, kernels and lightweight operating systems are commonplace. Such kernels and operating systems typically impose a thread based abstraction to concurrency. However, in general thread based programming is hard, plagued by hazards of race conditions and dead-locks. For this paper we take an alternative outset in terms of a language abstraction, RTFM-core, where the system is modelled directly in terms of tasks and resources. In compliance to the Stack Resource Policy (SRP) model, the language enforces (well formed) LIFO nesting of claimed resources, thus SRP based analysis and scheduling can be readily applied. For the execution onto bare-metal single core architectures, the rtfm-core compiler performs SRP analysis on the model, and render an executable that is deadlock free and (through RTFM-kernel primitives) exploits the underlying interrupt hardware for efficient scheduling. The RTFM-core language embeds C-code and links to C-object files and libraries, and is thus applicable to the mainstream of embedded development. However, while the language enforces well formed resource management, control flow in the embedded C-code may violate the LIFO nesting requirement, thus correctness is left with the programmer to ensure well formed nesting (through restricted control flow). In this paper we address this issue by lifting a subset of C into the RTFM-core language allowing arbitrary control flow at the model level. In this way well formed LIFO nesting can be enforced, and models ensured to be correct by construction. We demonstrate the feasibility trough a prototype implementation in the rtfm-core compiler. Additionally, we develop a set of running examples, and show in detail how control flow is handled at compile time and during run-time execution.
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| 9. |
- Moore, Josh, et al.
(författare)
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OME-Zarr : A cloud-optimized bioimaging file format with international community support
- 2023
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Ingår i: Histochemistry and Cell Biology. - : Springer Nature. - 1432-119X .- 0948-6143. ; 160:3, s. 223-251
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Tidskriftsartikel (refereegranskat)abstract
- A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing these problems have designed a format specification process (OME-NGFF) to address these needs. This paper brings together a wide range of those community members to describe the cloud-optimized format itself-OME-Zarr-along with tools and data resources available today to increase FAIR access and remove barriers in the scientific process. The current momentum offers an opportunity to unify a key component of the bioimaging domain-the file format that underlies so many personal, institutional, and global data management and analysis tasks.
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| 10. |
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