| 1. |
- Abarenkov, Kessy, et al.
(författare)
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Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden)
- 2016
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 16, s. 1-15
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Tidskriftsartikel (refereegranskat)abstract
- Recent molecular studies have identified substantial fungal diversity in indoor environments. Fungi and fungal particles have been linked to a range of potentially unwanted effects in the built environment, including asthma, decay of building materials, and food spoilage. The study of the built mycobiome is hampered by a number of constraints, one of which is the poor state of the metadata annotation of fungal DNA sequences from the built environment in public databases. In order to enable precise interrogation of such data – for example, “retrieve all fungal sequences recovered from bathrooms” – a workshop was organized at the University of Gothenburg (May 23-24, 2016) to annotate public fungal barcode (ITS) sequences according to the MIxS-Built Environment annotation standard (http://gensc.org/mixs/). The 36 participants assembled a total of 45,488 data points from the published literature, including the addition of 8,430 instances of countries of collection from a total of 83 countries, 5,801 instances of building types, and 3,876 instances of surface-air contaminants. The results were implemented in the UNITE database for molecular identification of fungi (http://unite.ut.ee) and were shared with other online resources. Data obtained from human/animal pathogenic fungi will furthermore be verified on culture based metadata for subsequent inclusion in the ISHAM-ITS database (http://its.mycologylab.org).
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| 2. |
- Mustafa, Dawan, 1985, et al.
(författare)
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The BGK Equation as the Limit of anN-Particle System
- 2020
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Ingår i: Journal of Statistical Physics. - : Springer Science and Business Media LLC. - 0022-4715 .- 1572-9613. ; 181, s. 715-737
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Tidskriftsartikel (refereegranskat)abstract
- The spatially homogeneous BGK equation is obtained as the limit of a model of a many particle system, similar to Mark Kac's charicature of the spatially homogeneous Boltzmann equation.
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| 3. |
- Lindsay, Willow, 1980, et al.
(författare)
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Endless forms of sexual selection
- 2019
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Ingår i: PeerJ. - : PeerJ. - 2167-8359. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- In recent years, the field of sexual selection has exploded, with advances in theoretical and empirical research complementing each other in exciting ways. This perspective piece is the product of a "stock-taking'' workshop on sexual selection and sexual conflict. Our aim is to identify and deliberate on outstanding questions and to stimulate discussion rather than provide a comprehensive overview of the entire field. These questions are organized into four thematic sections we deem essential to the field. First we focus on the evolution of mate choice and mating systems. Variation in mate quality can generate both competition and choice in the opposite sex, with implications for the evolution of mating systems. Limitations on mate choice may dictate the importance of direct vs. indirect benefits in mating decisions and consequently, mating systems, especially with regard to polyandry. Second, we focus on how sender and receiver mechanisms shape signal design. Mediation of honest signal content likely depends on integration of temporally variable social and physiological costs that are challenging to measure. We view the neuroethology of sensory and cognitive receiver biases as the main key to signal form and the 'aesthetic sense' proposed by Darwin. Since a receiver bias is sufficient to both initiate and drive ornament or armament exaggeration, without a genetically correlated or even coevolving receiver, this may be the appropriate 'null model' of sexual selection. Thirdly, we focus on the genetic architecture of sexually selected traits. Despite advances in modern molecular techniques, the number and identity of genes underlying performance, display and secondary sexual traits remains largely unknown. In-depth investigations into the genetic basis of sexual dimorphism in the context of long-term field studies will reveal constraints and trajectories of sexually selected trait evolution. Finally, we focus on sexual selection and conflict as drivers of speciation. Population divergence and speciation are often influenced by an interplay between sexual and natural selection. The extent to which sexual selection promotes or counteracts population divergence may vary depending on the genetic architecture of traits as well as the covariance between mating competition and local adaptation. Additionally, post-copulatory processes, such as selection against heterospecific sperm, may influence the importance of sexual selection in speciation. We propose that efforts to resolve these four themes can catalyze conceptual progress in the field of sexual selection, and we offer potential avenues of research to advance this progress.
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| 4. |
- Sundell, Håkan, 1968, et al.
(författare)
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NOBLE: non-blocking programming support via lock-free shared abstract data types
- 2009
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Ingår i: SIGARCH Computer Architecture News. - : ACM, Association for Computing Machinery, Inc.. - 0163-5964 .- 1943-5851. ; 36:5, s. 80-87
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Tidskriftsartikel (refereegranskat)abstract
- An essential part of programming for multi-core and multi-processor includes ef cient and reliable means for sharing data. Lock-free data structures are known as very suitable for this purpose, although experienced to be very complex to design. In this paper, we present a software library of non-blocking abstract data types that have been designed to facilitate lock-free programming for non-experts. The system provides: i) ef cient implementations of the most commonly used data types in concurrent and sequential software design, ii) a lock-free memory management system, and iii) a run time-system. The library provides clear semantics that are at least as strong as those of corresponding lock-based implementations of the respective data types. Our software library can be used for facilitating lockfree programming; its design enables the programmer to: i) replace lock-based components of sequential or parallel code easily and ef ciently , ii) use well-tuned concurrent algorithms inside a software or hardware transactional system. In the paper we describe the design and functionality of the system. We also provide experimental results that show that the library can considerably improve the performance of software systems.
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| 5. |
- Anderson, Dan, 1943, et al.
(författare)
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Approximate solution of a Thomas-Fermi model equation for bulk self-gravitating stellar objects in two dimensions
- 2017
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Ingår i: European journal of physics. - : Institute of Physics (IOP). - 0143-0807 .- 1361-6404. ; 38, s. 1-8
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Tidskriftsartikel (refereegranskat)abstract
- Direct variational methods are used to find simple approximate solutions of the Thomas–Fermi equations describing the properties of self-gravitating radially symmetric stellar objects both in the non-relativistic and ultra-relativistic cases. The approximate solutions are compared and shown to be in good agreement with exact and numerically obtained solutions.
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| 6. |
- Anderson, Dan, 1943, et al.
(författare)
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Introduction to direct variational and moment methods and an application to the Child-Langmuir law
- 2015
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Ingår i: European Journal of Physics. - : IOP Publishing. - 1361-6404 .- 0143-0807. ; 2015:36, s. 065032-
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Tidskriftsartikel (refereegranskat)abstract
- A short introduction is given of direct variational methods and its relation to Galerkin and moment methods, all flexible and powerful approaches for finding approximate solutions of difficult physical equations. A pedagogicalapplication of moment methods is given to the physically and technically important Child–Langmuir law in electron physics. The analysis is shown to provide simple, yet accurate, approximate solutions of the two-dimensionalproblem (a problem which does not allow an exact analytical solution)and illustrates the usefulness and the power of moment methods.
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| 7. |
- Gidenstam, Anders, et al.
(författare)
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Cache-Aware Lock-Free Queues for Multiple Producers/Consumers and Weak Memory Consistency
- 2010
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Ingår i: Proceedings of the 14th International Conference on Principles of Distributed Systems (OPODIS) 2010. - Berlin, Heidelberg : Springer. - 9783642176524 - 3642176526 ; 6490, s. 302-317
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Konferensbidrag (refereegranskat)abstract
- A lock-free FIFO queue data structure is presented in this paper. The algorithm supports multiple producers and multiple consumers and weak memory models. It has been designed to be cache-aware and work directly on weak memory models. It utilizes the cache behavior in concert with lazy updates of shared data, and a dynamic lock-free memory management scheme to decrease unnecessary synchronization and increase performance. Experiments on an 8-way multi-core platform show significantly better performance for the new algorithm compared to previous fast lock-free algorithms.
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| 8. |
- Gidenstam, Anders, 1977, et al.
(författare)
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Efficient and Reliable Lock-Free Memory Reclamation Based on Reference Counting
- 2009
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Ingår i: IEEE Transactions on Parallel and Distributed Systems. - : IEEE. - 1558-2183 .- 1045-9219. ; 20:8, s. 1173-1187
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Tidskriftsartikel (refereegranskat)abstract
- We present an efficient and practical lock-free method for semiautomatic (application-guided) memory reclamation based on reference counting, aimed for use with arbitrary lock-free dynamic data structures. The method guarantees the safety of local as well as global references, supports arbitrary memory reuse, uses atomic primitives that are available in modern computer systems, and provides an upper bound on the amount of memory waiting to be reclaimed. To the best of our knowledge, this is the first lock-free method that provides all of these properties. We provide analytical and experimental study of the method. The experiments conducted have shown that the method can also provide significant performance improvements for lock-free algorithms of dynamic data structures that require strong memory management.
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| 9. |
- Nguyen, Dang Nhan, 1983, et al.
(författare)
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Brief Announcement: ParMarkSplit: A Parallel Mark-Split Garbage Collector Based on a Lock-Free Skip-List
- 2013
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Ingår i: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). - : Springer. - 1611-3349 .- 0302-9743. - 9783642415265 ; 8205, s. 557-558
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Konferensbidrag (refereegranskat)abstract
- This brief announcement provides a high level overview of a parallel mark-split garbage collector. Our parallel design introduces and makes use of an efficient concurrency control mechanism based on a lock-free skip-list design for handling the list of free memory intervals. We have implemented the parallel mark-split garbage collector in OpenJDK HotSpot as a parallel and concurrent garbage collector for the old generation. We experimentally evaluate the collector and compare it with the default concurrent mark-sweep garbage collector in OpenJDK HotSpot, using the DaCapo benchmarks.
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| 10. |
- Nguyen, Dang Nhan, 1983, et al.
(författare)
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ParMarkSplit : A Parallel Mark-Split Garbage Collector Based on a Lock-Free Skip-List
- 2014
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Ingår i: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). - Cham : Springer. - 1611-3349 .- 0302-9743. - 9783319144719 - 9783319144726 ; 8878, s. 372-387
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Konferensbidrag (refereegranskat)abstract
- Mark-split is a garbage collection algorithm that combines advantages of both the mark-sweep and the copying collection algorithms. In this paper, we present a parallel mark-split garbage collector (GC). Our parallel design introduces and makes use of an efficient concurrency control mechanism for handling the list of free memory intervals. This mechanism is based on a lock-free skip-list design which supports an extended set of operations. Beside basic operations, it can perform a composite one that can search and remove and also insert two elements atomically. We have implemented the parallel mark-split GC in OpenJDK’s HotSpot virtual machine. We experimentally evaluate our collector and compare it with the default concurrent mark-sweep GC in HotSpot, using the DaCapo benchmarks, on two contemporary multiprocessor systems; one has 12 Intel Nehalem cores with HyperThreading and the other has 48 AMD Bulldozer cores. The evaluation shows that our parallel mark-split keeps the characteristics of the sequential mark-split, that it performs better than the concurrent mark-sweep in applications that have low live/garbage ratio, and have live objects locating contiguously, therefore being marked consecutively. Our parallel mark-split performs significantly better than a trivial parallelization based on locks in terms of both collection time and scalability.
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