| 1. |
- Zamora, Juan Carlos, et al.
(författare)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
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Ingår i: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
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Tidskriftsartikel (refereegranskat)abstract
- Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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| 2. |
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| 3. |
- Berg, Anders, et al.
(författare)
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Benefiting from an open-ended experiment? A comparison of attitudes to, and outcomes of, an expository versus an open-inquiry version of the same experiment
- 2003
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Ingår i: International Journal of Science Education. - : Informa UK Limited. - 0950-0693 .- 1464-5289. ; 25:3, s. 351-372
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Tidskriftsartikel (refereegranskat)abstract
- In this article we compare outcomes of an open-inquiry and an expository version of a chemistry laboratory experiment at university level for 190 students. The aim of the study was to investigate if these two versions would result in different outcomes depending on the students' attitudes towards learning. We used a questionnaire to find out their attitude position prior to the laboratory experiment. The outcome in the different version of the experiment was evaluated by interviews, questions asked during the experiment and students self-evaluations. The main findings were that the open-inquiry version shows the most positive outcomes regarding learning outcome, preparation time, time spent in the laboratory and student perception of the experiment. The students with low attitude position needed more support to meet the challenge of an open-inquiry experiment, the support being a clearer explanation of the aims, and feedback from the instructor during the experiment.
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| 4. |
- Bivall, Petter, 1979-
(författare)
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Touching the Essence of Life : Haptic Virtual Proteins for Learning
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This dissertation presents research in the development and use of a multi-modal visual and haptic virtual model in higher education. The model, named Chemical Force Feedback (CFF), represents molecular recognition through the example of protein-ligand docking, and enables students to simultaneously see and feel representations of the protein and ligand molecules and their force interactions. The research efforts have been divided between educational research aspects and development of haptic feedback techniques.The CFF model was evaluated in situ through multiple data-collections in a university course on molecular interactions. To isolate possible influences of haptics on learning, half of the students ran CFF with haptics, and the others used the equipment with force feedback disabled. Pre- and post-tests showed a significant learning gain for all students. A particular influence of haptics was found on students reasoning, discovered through an open-ended written probe where students' responses contained elaborate descriptions of the molecular recognition process.Students' interactions with the system were analyzed using customized information visualization tools. Analysis revealed differences between the groups, for example, in their use of visual representations on offer, and in how they moved the ligand molecule. Differences in representational and interactive behaviours showed relationships with aspects of the learning outcomes.The CFF model was improved in an iterative evaluation and development process. A focus was placed on force model design, where one significant challenge was in conveying information from data with large force differences, ranging from very weak interactions to extreme forces generated when atoms collide. Therefore, a History Dependent Transfer Function (HDTF) was designed which adapts the translation of forces derived from the data to output forces according to the properties of the recently derived forces. Evaluation revealed that the HDTF improves the ability to haptically detect features in volumetric data with large force ranges.To further enable force models with high fidelity, an investigation was conducted to determine the perceptual Just Noticeable Difference (JND) in force for detection of interfaces between features in volumetric data. Results showed that JNDs vary depending on the magnitude of the forces in the volume and depending on where in the workspace the data is presented.
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| 5. |
- Bivall Persson, Petter, 1979-, et al.
(författare)
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Designing and Evaluating a Haptic System for Biomolecular Education
- 2007
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Ingår i: IEEE Virtual Reality Conference, 2007. VR '07.. - Piscataway, NJ, USA : IEEE. - 1424409063 ; , s. 171-178
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Konferensbidrag (refereegranskat)abstract
- In this paper we present an in situ evaluation of a haptic system, with a representative test population, we aim to determine what, if any, benefit haptics can have in a biomolecular education context. We have developed a haptic application for conveying concepts of molecular interactions, specifically in protein-ligand docking. Utilizing a semi-immersive environment with stereo graphics, users are able to manipulate the ligand and feel its interactions in the docking process. The evaluation used cognitive knowledge tests and interviews focused on learning gains. Compared with using time efficiency as the single quality measure this gives a better indication of a system's applicability in an educational environment. Surveys were used to gather opinions and suggestions for improvements. Students do gain from using the application in the learning process but the learning appears to be independent of the addition of haptic feedback. However the addition of force feedback did decrease time requirements and improved the students understanding of the docking process in terms of the forces involved, as is apparent from the students' descriptions of the experience. The students also indicated a number of features which could be improved in future development.
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| 6. |
- Bivall Persson, Petter, 1979-, et al.
(författare)
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Evaluating the Effectiveness of Haptic Visualization in Biomolecular Education - Feeling Molecular Specificity in a Docking Task
- 2006
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Ingår i: 12th IOSTE Symposium. - : Universiti Science Malaysia. - 9832700396 ; , s. 745-752
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Konferensbidrag (refereegranskat)abstract
- Within the molecular life sciences extensive use is made of visual representations, ranging from sketches to advanced computer graphics, often used to convey abstract knowledge that is difficult for the student to grasp. This work evaluates a new visual and haptic (tactile/kinetic) tool for protein docking in an in situ learning situation by combining qualitative and quantitative methods, performing tests and interviews with students; all aiming at a proper inclusion of visualization tools into biomolecular education. Preliminary results indicate time gains, strong positive affective responses and learning gains from the tasks, however the influence of haptics needs further investigation.
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| 7. |
- Bivall Persson, Petter, 1979-, et al.
(författare)
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Improved Feature Detection over Large Force Ranges Using History Dependent Transfer Functions
- 2009
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Ingår i: Third Joint Eurohaptics Conference and Symposium on Haptic Interfaces for Virtual Environments and Teleoperator Systems, WorldHaptics 2009. - : IEEE. - 9781424438587 ; , s. 476-481
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Konferensbidrag (refereegranskat)abstract
- In this paper we present a history dependent transfer function (HDTF) as a possible approach to enable improved haptic feature detection in high dynamic range (HDR) volume data. The HDTF is a multi-dimensional transfer function that uses the recent force history as a selection criterion to switch between transfer functions, thereby adapting to the explored force range. The HDTF has been evaluated using artificial test data and in a realistic application example, with the HDTF applied to haptic protein-ligand docking. Biochemistry experts performed docking tests, and expressed that the HDTF delivers the expected feedback across a large force magnitude range, conveying both weak attractive and strong repulsive protein-ligand interaction forces. Feature detection tests have been performed with positive results, indicating that the HDTF improves the ability of feature detection in HDR volume data as compared to a static transfer function covering the same range.
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| 8. |
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| 9. |
- Carlson, R. F., et al.
(författare)
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A method for measuring light ion reaction cross-sections
- 2005
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Ingår i: Nuclear Instruments and Methods in Physics Research Section A. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 547:2-3, s. 541-554
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Tidskriftsartikel (refereegranskat)abstract
- An experimental procedure for measuring reaction cross-sections of light ions in the energy range 20 50 MeV/nucleon, using a modified attenuation technique, is described. The detection method incorporates a forward detector that simultaneously measures the reaction cross-sections for five different sizes of the solid angle in steps from 99.1% to 99.8% of the total solid angle. The final reaction cross-section values are obtained by extrapolation to the full solid angle.
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| 10. |
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| 11. |
- Eriksson, Olof, et al.
(författare)
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Positron emission tomography in clinical islet transplantation
- 2009
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Ingår i: American Journal of Transplantation. - : Elsevier BV. - 1600-6135 .- 1600-6143. ; 9:12, s. 2816-2824
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Tidskriftsartikel (refereegranskat)abstract
- The fate of islets in clinical transplantation is unclear. To elude on this positron emission tomography combined with computed tomography (PET/CT) was performed for 60 min during islet transplantation in five patients receiving six transplants. A fraction of the islets (23%) were labeled with 18F-fluorodeoxyglucose ([(18)F]FDG) and carefully mixed with unlabeled islets just prior to intraportal transplantation. The peak radioactivity concentration in the liver was found at 19 min after start of islet infusion and corresponded to only 75% of what was expected, indicating that islets are lost during the transplantation procedure. No accumulation of radioactivity was found in the lungs. A nonphysiological peak of C-peptide was found in plasma during and immediately after transplantation in all subjects. Distribution in the liver was heterogeneous with wide variations in location and concentration. Islets found in areas with concentrations of >400 IEQ/cc liver tissue varied between 1% and 32% of the graft in different subjects. No side effects attributed to the PET/CT procedure were found. Clinical outcome in all patients was comparable to that previously observed indicating that the [(18)F]FDG labeling procedure did not harm the islets. The technique has potential to be used to assess approaches to enhance islet survival and engraftment in clinical transplantation.
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| 12. |
- Heidmarsson, Starri, et al.
(författare)
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Classification of lichen photomorphs
- 1997
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Ingår i: Taxon. - : Wiley. - 0040-0262 .- 1996-8175. ; :46, s. 519-520
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Tidskriftsartikel (refereegranskat)
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| 13. |
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| 14. |
- Nordin, Anders, et al.
(författare)
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A preliminary phylogeny of Aspicilia in relation to morphological and secondary product variation
- 2007
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Ingår i: Lichenologische Nebenstunden. - 9783443580759 ; , s. 247-266
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Bokkapitel (refereegranskat)abstract
- A preliminary molecular phylogeny of 26 Aspicilia species based on nuclear rDNA ITS1-5.8S-ITS2 is presented and compared with the occurrence of some morphological features and secondary chemical products. Three major monophyletic groups were discovered, one including aspicilin-containing species with large spores and short conidia, a second with mainly arctic-alpine species with small spores, variable chemistry and conidium length, and a third group having spores of variable size, conidia of medium size and containing β-orcinol depsidones. An extended analysis of the second subgroup, including additional species and sequences, resulted in the synonymization of a number of names. Lectotypes are designated for A. mashiginensis, A. mastrucata, A. obscurata and A. permutata, and the lectotypification of A. verruculosa is discussed.
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| 15. |
- Nordin, Anders, et al.
(författare)
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Additional species in Tetramelas
- 2005
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Ingår i: The Lichenologist. - 0024-2829. ; 37:6, s. 491-498
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Tidskriftsartikel (populärvet., debatt m.m.)abstract
- Tetramelas phaeophysciae, a new obligately lichenicolous species occurring in Scandinavia, Iceland and Greenland, is described, and the closely related Buellia pulverulenta, together with B. triphramgioides, are transferred to Tetramelas. Phylogenetic reconstructions based on sequence data from nITS1-5.8S-ITS2 rDNA, using Bayesian inference and parsimony analyses, support the segregation of the new species from B. pulverulenta as well as the segregation of Tetramelas and Diplotomma from Buellia s. str.
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| 16. |
- Nordin, Anders, et al.
(författare)
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Aspicilia berntii, a new name for a poorly known species
- 2008
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Ingår i: The Lichenologist. - 0024-2829. ; 40:2, s. 127-133
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Tidskriftsartikel (populärvet., debatt m.m.)abstract
- The new name Aspicilia berntii is proposed to accomodate Lecanora mastoidea Lynge in Aspicilia and a lectotype is designated. Additional characters are added to the species description and a comparison is made with similar species. The species is reported as new to Scandinavia with localities in northern Norway. An assessement of the phylogenetic relationships, based on a split network analysis of ITS sequences, places A. berntii close to A. verrucigera in the A. cinerea group
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| 17. |
- Nordin, Anders, 1949-, et al.
(författare)
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Endocarpon moenium belongs in Acarosporaceae
- 2009
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Ingår i: Graphis Scripta. - Stockholm : Nordisk Lichenologisk Förening. - 0901-7593. ; 21:1, s. 21-22
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Tidskriftsartikel (refereegranskat)abstract
- ITS, LSU and mtSSU sequences indicate that Endocarpon moenium belongs in Acarosporaceae. The name Acarospora moenium (Vain.) Räsänen is available and could be adopted awaiting a more definite placement of the species.
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| 18. |
- Nordin, Anders, et al.
(författare)
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Phylogeny and taxonomy of Aspicilia and Megasporaceae
- 2010
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Ingår i: Mycologia. - : Informa UK Limited. - 0027-5514 .- 1557-2536. ; 102:6, s. 1339-1349
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Tidskriftsartikel (refereegranskat)abstract
- Phylogenetic analyses based on nuLSU and mtSSU indicate that Megasporaceae is monophyletic. Aspicilia species were distributed among three main well supported groups and one group with low support that included the type species; a division of the family into five genera is proposed. The old names Circinaria and Sagedia are reintroduced for groups not including A. cinerea, the type of Aspicilia. The monotypic Megaspora is closely related to Circinaria, while Lobothallia is the sister group of the other Megasporaceae genera. Aspicilia recedens and A. farinosa are transferred to Lobothallia. Species of the 'Sphaerothallia group' are nested in Circinaria. Aspilidea is not a member of Megasporaceae but seems to be more closely related to Ochrolechiaceae. Aspilidea myrinii is neotypified, and lectotypes are designated for Aspicilia gibbosa, A. leprosescens and Lecanora gibbosula.
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| 19. |
- Nordin, Anders, et al.
(författare)
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Two new Aspicilia species from Fennoscandia and Russia
- 2011
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Ingår i: The Lichenologist. - 0024-2829 .- 1096-1135. ; 43:1, s. 27-37
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Tidskriftsartikel (refereegranskat)abstract
- Aspicilia fluviatilis and A. granulosa, two arctic and/or (sub) alpine species with elongate +/- diverging and +/- branching marginal areoles, are described as new and compared with similar species occurring in Fennoscandia. A parsimony analysis based on ITS indicates a close relationship with the mainly coastal A. epiglypta. Aspicilia epiglypta, A. disserpens and A. sublapponica are lectotypified and A. disserpens is reduced to synonymy with A. perradiata. Aspicilia alboradiata and A. circularis are excluded from the Fennoscandian lichen biota. A key to Fennoscandian Aspicilia species with radiating thalli and/or elongate +/- diverging and +/- branching marginal areoles is also presented.
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| 20. |
- Owe-Larsson, Björn, et al.
(författare)
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Aspicilia
- 2007
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Ingår i: Lichen Flora of the Greater Sonoran Desert Region. - Tempe : Lichens Unlimited, Arizona State University.
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Bokkapitel (refereegranskat)
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| 21. |
- Owe-Larsson, Björn, et al.
(författare)
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Aspicilia
- 2008
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Ingår i: Lichen Flora of the Greater Sonoran Desert Region, vol. 3.. - Tempe : Lichens Unlimited, Arizona State University. - 0971675910 ; , s. 61-108
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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| 22. |
- Owe-Larsson, Björn, et al.
(författare)
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Circinaria arida spec. nova and the ‘Aspicilia desertorum’ complex
- 2011
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Ingår i: Biomonitoring, Ecology, and Systematics of Lichens. - Berlin/Stuttgart : J. Cramer. - 9783443580858 ; , s. 235-246
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Bokkapitel (refereegranskat)abstract
- Circinaria arida sp. nova is described from the Sonoran area. In the Sonoran Desert Lichen Flora 3 it was tentatively treated as Aspicilia desertorum. This name, however, is based on Lecanora desertorum, an illegitimate name introduced by Krempelhuber for both vagrant and saxicolous taxa, but usually only applied to non-vagrant, saxicolous specimens. In the analysis presented here these are shown to represent more than one taxon. For American specimens the epithet elmorei is available, and the combination Circinaria elmorei is proposed.
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| 23. |
- Paukov, Alexander, et al.
(författare)
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Aspicilia goettweigensis (Megasporaceae, lichenized Ascomycetes) – a poorly known and overlooked species in Europe and Russia
- 2017
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Ingår i: Nordic Journal of Botany. - : Wiley. - 0107-055X .- 1756-1051. ; 35:5, s. 595-601
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Tidskriftsartikel (refereegranskat)abstract
- Aspicilia goettweigensis is a poorly known species from xerothermic siliceous rocks in Europe. It is considered to be common in the Czech Republic and it is new to Hungary and Russia. The main diagnostic character is formation of cracked, popcorn-like, areoles in the central parts of the thalli. Analysis of nrITS sequences revealed its close relationship to Aspicilia subdepressa and A. volcanica. TLC revealed stictic acid in analysed A. goettweigensis samples. A key to non-lobate Aspicilia with stictic acid known from Europe is provided.
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| 24. |
- Ringbom, Anders, et al.
(författare)
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The Pb-208(n,p)Tl-208 reaction at E-n=97 MeV
- 1997
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Ingår i: NUCLEAR PHYSICS A. - : ELSEVIER SCIENCE BV. - 0375-9474. ; 617:3, s. 316-330
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Tidskriftsartikel (refereegranskat)abstract
- Double-differential cross sections of the Pb-208(n,p) reaction have been measured at 97 MeV in the angular range 0 degrees-30 degrees for excitation energies up to 40 MeV. The experimental proton spectra have been compared with calculated spectra obtained
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| 25. |
- Roux, Claude, et al.
(författare)
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Quelques espèces d’Aspicilia peu connues ou nouvelles des Pyrénées-Orientales
- 2011
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Ingår i: Bulletin de la Société linnéenne de Provence. Numéro spécial. - 0373-0875. ; :14, s. 177-227
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Tidskriftsartikel (refereegranskat)abstract
- The nomenclature of the Aspicilia anatomy is reconsidered and six species are described. Two of these are new to science (A. calcitrapa and A. prestensis), two are poorly known (A. spermatomanes and A. subdepressa), one is new to Europe (A. brucei), and one is very variable and often confused with other species (A. cinerea). The phylogenetic relationships are assessed by use of PAUP and SplitsTree analyses based on ITS data. In an appendix A. bricconensis discussed.
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| 26. |
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| 27. |
- Tønsberg, Tor, et al.
(författare)
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Amandinea lignicola, a new species from the Pacific coast of North America
- 2012
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Ingår i: Graphis Scripta. - 0901-7593. ; 24:2, s. 60-64
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Tidskriftsartikel (refereegranskat)abstract
- Amandinea lignicola is described from Washington, USA, and British Columbia,Canada, on the Pacific coast of North America where it is lignicolous ondriftwood. The presence of soredia makes it distinct from all other speciescurrently assigned to Amandinea.
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| 28. |
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| 29. |
- Valadbeigi, Tahereh, et al.
(författare)
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Megaspora rimisorediata (Pertusariales, Megasporaceae), a new sorediate species from Iran and its affinities with Aspicilia sensu lato
- 2011
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Ingår i: The Lichenologist. - 0024-2829 .- 1096-1135. ; 43:4, s. 285-291
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Tidskriftsartikel (refereegranskat)abstract
- The new species Megaspora rimisorediata Valadbeigi & A. Nordin is described from Iran, where it mainly grows on tree bark but also on calciferous rocks and mosses. It is characterized by a pale ochraceous to bluish grey, cracked and sorediate thallus, very rarely producing ascomata. It appears to be rather commonly distributed in Iran. Its close affinity with Megaspora verrucosa is illustrated in a graph resulting from a phylogenetic network analysis of nuclear rDNA ITS1-5.8S-ITS2 sequences from specimens representing the different genera of Megasporaceae.
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| 30. |
- Ynnerman, Anders, et al.
(författare)
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Exploranation: A New Science Communication Paradigm
- 2018
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Ingår i: IEEE Computer Graphics and Applications. - : IEEE COMPUTER SOC. - 0272-1716 .- 1558-1756. ; 38:3, s. 13-20
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Science communication is facing a paradigm shift, based on the convergence of exploratory and explanatory visualization. In this article, we coin the term exploranation to denote the way in which visualization methods from scientific exploration can be used to communicate results and how methods in explanatory visualization can enrich exploration.
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