| 1. |
- Schwenk, Jochen M., et al.
(författare)
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Toward Next Generation Plasma Profiling via Heat-induced Epitope Retrieval and Array-based Assays
- 2010
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Ingår i: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 9:11, s. 2497-2507
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Tidskriftsartikel (refereegranskat)abstract
- There is a need for high throughput methods for screening patient samples in the quest for potential biomarkers for diagnostics and patient care. Here, we used a combination of undirected target selection, antibody suspension bead arrays, and heat-induced epitope retrieval to allow for protein profiling of human plasma in a novel and systematic manner. Several antibodies were found to reveal altered protein profiles upon epitope retrieval at elevated temperatures with limits of detection improving into lower ng/ml ranges. In a study based on prostate cancer patients, several proteins with differential profiles were discovered and subsequently validated in an independent cohort. For one of the potential biomarkers, the human carnosine dipeptidase 1 protein (CNDP1), the differences were determined to be related to the glycosylation status of the targeted protein. The study shows a path of pursuit for large scale screening of biobank repositories in a flexible and proteome-wide fashion by utilizing heat-induced epitope retrieval and using an antibody suspension bead array format. Molecular & Cellular Proteomics 9:2497-2507, 2010.
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| 2. |
- Ruta, C., et al.
(författare)
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Phylogeny of Hesionidae (Aciculata, Polychaeta), assessed from morphology, 18S rDNA, 28S rDNA, 16S rDNA and COI
- 2007
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Ingår i: Zoologica Scripta. - : Wiley. - 0300-3256 .- 1463-6409. ; 36:1, s. 99-107
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Tidskriftsartikel (refereegranskat)abstract
- We assess phylogenetic relationships within the polychaete family Hesionidae from morphological data combined with nucleotide data from 18S rDNA, 28S rDNA, 16S rDNA and COI. Parsimony and Bayesian analyses were performed on two data sets; the first was based on a more restricted set of terminals with both morphological and molecular data (17 ingroup terminals), while the second included additional taxa with morphological data only (25 ingroup terminals). The different sets of terminals yielded fully congruent results, as did the parsimony and the Bayesian analyses. Our results indicate high levels of homoplasy in traditionally used morphological characters in the group, and that Hesioninae, Gyptini and Gyptis are nonmonophyletic. Hesionini (mainly Hesione and Leocrates), Psamathini (mainly Hesiospina, Micropodarke, Nereimyra, Psamathe and Syllidia), Ophiodrominae (Gyptini and Ophiodromini) and Ophiodromini (mainly Heteropodarke, Ophiodromus and Podarkeopsis) are monophyletic and agree with previous classifications, and Hesionini is probably the sister to all other hesionids. The placements of the small hesionids capricornia and Lizardia, the hydrothermal vent taxa Hesiodeira and Hesiolyra, and the newly described Hesiobranchia, remain uncertain.
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| 3. |
- Wiklund Lindström, Susanne, et al.
(författare)
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The importance of balanced data sets for partial least squares discriminant analysis : classification problems using hyperspectral imaging data
- 2011
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Ingår i: Journal of Near Infrared Spectroscopy. - : IM Publications. - 0967-0335 .- 1751-6552. ; 19:4, s. 233-241
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Tidskriftsartikel (refereegranskat)abstract
- This study investigates the effect of imbalanced spectral data in the training set, when developing partial least squares discriminant analysis (PLS-DA) classification models for use in future predictions. The experimental study was performed using a real hyperspectral short-wavelength infrared image data set collected from bakery products (buns) containing contaminants (flies) but similar applications for other insects, paper and plastic were also tested. The contaminants represent a very small proportion of the images relative to the bun. The PLS-DA model aims at accurately detecting and classifying the contaminants and this requires a modification of the calibration data set. The paper deals with problems caused by unbalanced calibration data sets and how to remedy them. In the example it was demonstrated that, by balancing the calibration data from 58,476 bun pixels + 279 fly pixels to 279 bun + 279 fly pixels, the number of true predictions could be improved with a smaller number of PLS components used in the model. The improvement for flies increased from 65% true predictions with ten PLS components to >99% true prediction with five to six PLS components. The true prediction for bun went from 100% to 99.5% with six PLS components which is an acceptable reduction. Theoretical explanations are included.
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| 4. |
- Spjuth, Ola, 1977-, et al.
(författare)
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E-Science technologies in a workflow for personalized medicine using cancer screening as a case study
- 2017
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Ingår i: JAMIA Journal of the American Medical Informatics Association. - : Oxford University Press. - 1067-5027 .- 1527-974X. ; 24:5, s. 950-957
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Tidskriftsartikel (refereegranskat)abstract
- Objective: We provide an e-Science perspective on the workflow from risk factor discovery and classification of disease to evaluation of personalized intervention programs. As case studies, we use personalized prostate and breast cancer screenings.Materials and Methods: We describe an e-Science initiative in Sweden, e-Science for Cancer Prevention and Control (eCPC), which supports biomarker discovery and offers decision support for personalized intervention strategies. The generic eCPC contribution is a workflow with 4 nodes applied iteratively, and the concept of e-Science signifies systematic use of tools from the mathematical, statistical, data, and computer sciences.Results: The eCPC workflow is illustrated through 2 case studies. For prostate cancer, an in-house personalized screening tool, the Stockholm-3 model (S3M), is presented as an alternative to prostate-specific antigen testing alone. S3M is evaluated in a trial setting and plans for rollout in the population are discussed. For breast cancer, new biomarkers based on breast density and molecular profiles are developed and the US multicenter Women Informed to Screen Depending on Measures (WISDOM) trial is referred to for evaluation. While current eCPC data management uses a traditional data warehouse model, we discuss eCPC-developed features of a coherent data integration platform.Discussion and Conclusion: E-Science tools are a key part of an evidence-based process for personalized medicine. This paper provides a structured workflow from data and models to evaluation of new personalized intervention strategies. The importance of multidisciplinary collaboration is emphasized. Importantly, the generic concepts of the suggested eCPC workflow are transferrable to other disease domains, although each disease will require tailored solutions.
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| 5. |
- Norlinder, Erika, 1977, et al.
(författare)
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Phylogeny of scale-worms (Aphroditiformia, Annelida), assessed from 18SrRNA, 28SrRNA, 16SrRNA, mitochondrial cytochrome c oxidase subunit I (COI), and morphology
- 2012
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903. ; 65:2, s. 490-500
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Tidskriftsartikel (refereegranskat)abstract
- The phylogeny of scale-worms, benthic polychaetes carrying dorsal scales (elytra), including taxa from Acoetidae, Aphroditidae, Eulepethidae, Pholoidae, Pholoididae, Polynoidae and Sigalionidae (Aphroditiformia), is assessed from the nuclear markers 18SrRNA and 28SrRNA, and mitochondrial 16SrRNA and cytochrome c oxidase subunit I (COI), and 24 morphological characters. The data sets are analyzed both separately and combined, with Bayesian analyses, maximum likelihood and parsimony. In total, 56 terminal taxa are examined, including 48 taxa from all scale-worm families, and eight out-group species. The results indicate that Aphroditidae and Eulepethidae are the most basally placed families among the scale-worms. The Pholoididae and Pisionidae are positioned within and synonymized with the Sigalionidae, and Pholoidae may be part of the same group. The subfamily Iphioninae falls out as sister group to a clade consisting of Polynoidae and Acoetidae and is elevated to Iphionidae. The families now included in the Aphroditiformia are Acoetidae, Aphroditidae, Eulepethidae, Pholoidae, Polynoidae, Iphionidae and Sigalionidae, and the subfamily name Harmothoinae and Acholoinae are treated as a junior synonyms of Polynoinae. (C) 2012 Published by Elsevier Inc.
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| 6. |
- Pleijel, Fredrik, 1955, et al.
(författare)
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Vrijenhoekia balaenophila, a new hesionid polychaete from a whale fall off CaliforniaVrijenhoekia balaenophila, a new hesionid polychaete from a whale fall off California
- 2008
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Ingår i: Zoological Journal of the Linnean Society. - : Oxford University Press (OUP). - 0024-4082 .- 1096-3642. ; 152:4, s. 625-634
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Tidskriftsartikel (refereegranskat)abstract
- Vrijenhoekia balaenophila gen. nov., sp. nov. (Polychaeta, Hesionidae) is described from a whale carcass at near 3000 m depth in Monterey Canyon off the coast of California. The phylogenetic relationships of V. balaenophila are assessed in a parsimony analysis of morphological data together with nucleotide data from 28S rDNA, 16S rDNA and cytochrome oxidase I genes. Within the hesionids V. balaenophila belongs to Psamathini, where it is the sister group to Sirsoe. Among psamathins it is morphologically distinguished by having six glandular lip pads around the mouth opening, papilla-shaped neuropodial lobes on segment 3, extreme length of the dorsal cirri, and by a characteristic growth pattern in which the maximum number of segments is already formed in subadults, and further growth takes place through size increase of the segments.
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| 7. |
- Wiklund, Helena, 1965, et al.
(författare)
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Phylogeny of Aphroditiformia (Polychaeta) based on molecular and morphological data
- 2005
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903. ; 37:2, s. 494-502
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Tidskriftsartikel (refereegranskat)abstract
- The phylogeny of Aphroditiformia, benthic polychaetes carrying dorsal elytra, is assessed from nuclear 18S rDNA, mitochondrial cytochrome c oxidase subunit I (COI), and 31 morphological characters. Two non-elytrabearing taxa, Palmyra and Pisione, are included to assess their relationship to the elytrabearers. The data are analysed both separately and combined, with parsimony, maximum likelihood and Bayesian analyses. In total, 19 terminal taxa are examined, including 12 elytrabearing taxa from all scale-worm groups, Palmyra, Pisione, and five outgroup taxa. The results show that Palmyra and Pisione are nested within Aphroditiformia. Palmyra is sister to Aphrodita, and both Pisione and Pholoe are positioned within Sigalionidae, suggesting that both family names Pisionidae and Pholoidae should be treated as junior synonyms of Sigalionidae. (c) 2005 Elsevier Inc. All rights reserved.
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| 8. |
- Bailey-Wilson, Joan E, et al.
(författare)
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Analysis of Xq27-28 linkage in the international consortium for prostate cancer genetics (ICPCG) families
- 2012
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Ingår i: BMC Medical Genetics. - London : BioMed Central. - 1471-2350. ; 13, s. 46-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Genetic variants are likely to contribute to a portion of prostate cancer risk. Full elucidation of the genetic etiology of prostate cancer is difficult because of incomplete penetrance and genetic and phenotypic heterogeneity. Current evidence suggests that genetic linkage to prostate cancer has been found on several chromosomes including the X; however, identification of causative genes has been elusive.Methods: Parametric and non-parametric linkage analyses were performed using 26 microsatellite markers in each of 11 groups of multiple-case prostate cancer families from the International Consortium for Prostate Cancer Genetics (ICPCG). Meta-analyses of the resultant family-specific linkage statistics across the entire 1,323 families and in several predefined subsets were then performed.Results: Meta-analyses of linkage statistics resulted in a maximum parametric heterogeneity lod score (HLOD) of 1.28, and an allele-sharing lod score (LOD) of 2.0 in favor of linkage to Xq27-q28 at 138 cM. In subset analyses, families with average age at onset less than 65 years exhibited a maximum HLOD of 1.8 (at 138 cM) versus a maximum regional HLOD of only 0.32 in families with average age at onset of 65 years or older. Surprisingly, the subset of families with only 2-3 affected men and some evidence of male-to-male transmission of prostate cancer gave the strongest evidence of linkage to the region (HLOD = 3.24, 134 cM). For this subset, the HLOD was slightly increased (HLOD = 3.47 at 134 cM) when families used in the original published report of linkage to Xq27-28 were excluded.Conclusions: Although there was not strong support for linkage to the Xq27-28 region in the complete set of families, the subset of families with earlier age at onset exhibited more evidence of linkage than families with later onset of disease. A subset of families with 2-3 affected individuals and with some evidence of male to male disease transmission showed stronger linkage signals. Our results suggest that the genetic basis for prostate cancer in our families is much more complex than a single susceptibility locus on the X chromosome, and that future explorations of the Xq27-28 region should focus on the subset of families identified here with the strongest evidence of linkage to this region.
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| 9. |
- Karlsson, Bengt, et al.
(författare)
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Test of a developmental trade-off in a polyphenic butterfly: direct development favours reproductive output
- 2008
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Ingår i: Functional Ecology. - : Wiley. - 0269-8463 .- 1365-2435. ; 22:1, s. 121-126
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Tidskriftsartikel (refereegranskat)abstract
- 1.Evolutionary theory predicts that resource allocation decisions taken during development are adjusted to an organism's life-history. These decisions may have irreversible effects on body design and strong fitness consequences. Holometabolous insects that have a long expected life span typically postpone reproduction, and so are expected to allocate resources for somatic maintenance prior to investing in reproduction. In contrast, insects that have a short expected life span are expected to allocate relatively less to soma and more to reproduction. In support of this theory, an earlier investigation of resources allocated to soma vs. reproductive reserves in the comma butterfly, Polygonia c-album, revealed that short-lived females indeed allocate more resources to reproductive reserves as compared to longer lived females that hibernate before reproduction suggesting that short-lived females should have higher fecundity. 2. Here we test this prediction, using the comma butterfly as our study organism. Depending on daylength and temperature this butterfly produces one of two morphs: (i) a light summer morph that reproduces directly after adult eclosion and has a short expected life span of a couple of weeks; or (ii) a darker winter morph that normally lives for 8–9 months before the onset of reproduction. Our test is based on experimental manipulation that allowed us to induce reproduction without prior hibernation in winter morph comma butterflies, and comparing lifetime fecundity among three groups: (i) directly reproducing summer morph commas; (ii) directly reproducing winter morph commas; and (iii) winter morph commas reproducing after overwintering. This protocol allowed us to tease apart trade-offs during development and the hibernation period. 3. The results showed that the short-lived summer morph had a substantially higher fecundity (total number of eggs = 586 ± 19, mean ± SE) than the winter morph females manipulated to reproduce without hibernation (total number of eggs = 334 ± 42). We argue that this is a consequence of a resource allocation trade-off during early development observed in this species; females with a short expected life as adults allocate relatively more of their resources to reproductive parts and thereby reach a higher reproductive output compared to females predisposed for a long adult life. 4. There was no significant difference in lifetime fecundity between winter morph females that did, or did not, hibernate before reproduction. This suggests that the cost of hibernation per se is small and hence corroborates our conclusion that the life-history implemented trade-off made during early development underlies the lower reproductive output of the winter morph butterflies.
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| 10. |
- Nygren, Arne, 1971, et al.
(författare)
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Bertil Åkesson (1928-2013) obituary.
- 2014
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Ingår i: Memoires of Museum Victoria. - 1447-2546 .- 1447-2554. ; 71, s. 343-345
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
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