| 1. |
- Andersson, Leif, et al.
(författare)
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How Fish Population Genomics Can Promote Sustainable Fisheries : A Road Map
- 2024
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Ingår i: Annual Review of Animal Biosciences. - : ANNUAL REVIEWS. - 2165-8102 .- 2165-8110. ; 12, s. 1-20
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Forskningsöversikt (refereegranskat)abstract
- Maintenance of genetic diversity in marine fishes targeted by commercial fishing is a grand challenge for the future. Most of these species are abundant and therefore important for marine ecosystems and food security. Here, we present a road map of how population genomics can promote sustainable fisheries. In these species, the development of reference genomes and whole genome sequencing is key, because genetic differentiation at neutral loci is usually low due to large population sizes and gene flow. First, baseline allele frequencies representing genetically differentiated populations within species must be established. These can then be used to accurately determine the composition of mixed samples, forming the basis for population demographic analysis to inform sustainably set fish quotas. SNP-chip analysis is a cost-effective method for determining baseline allele frequencies and for population identification in mixed samples. Finally, we describe how genetic marker analysis can transform stock identification and management.
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| 2. |
- Hallösta, Simon, 1994-, et al.
(författare)
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Effects of Foreground Augmentations in Synthetic Training Data on the Use of UAVs for Weed Detection
- 2024
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Ingår i: Proceedings of Machine Learning Research. - : ML Research Press.
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Konferensbidrag (refereegranskat)abstract
- This study addresses the issue of black-grass, a herbicide-resistant weed that threatens wheat yields in Western Europe, through the use of high- resolution Unmanned Aerial Vehicles (UAVs) and synthetic data augmentation in precision agriculture. We mitigate challenges such as the need for large labeled datasets and environmental variability by employing synthetic data augmentations in training a Mask R-CNN model. Using a minimal dataset of 43 black-grass and 12 wheat field images, we achieved a 37% increase in Area Under the Curve (AUC) over the non-augmented baseline, with scaling as the most effective augmentation. The best model attained a recall of 53% at a precision of 64%, offering a promising approach for future precision agriculture applications. © NLDL 2024. All rights reserved.
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| 3. |
- Hallösta, Simon, 1994-, et al.
(författare)
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Impact of Neural Network Architecture for Fingerprint Recognition
- 2024
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Ingår i: Intelligent Systems and Pattern Recognition. - : Springer. - 9783031463341 - 9783031463358 ; , s. 3-14
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Konferensbidrag (refereegranskat)abstract
- This work investigates the impact of the neural networks architecture when performing fingerprint recognition. Three networks are studied; a Triplet network and two Siamese networks. They are evaluated on datasets with specified amounts of relative translation between fingerprints. The results show that the Siamese model based on contrastive loss performed best in all evaluated metrics. Moreover, the results indicate that the network with a categorical scheme performed inferior to the other models, especially in recognizing images with high confidence. The Equal Error Rate (EER) of the best model ranged between 4%−11% which was on average 6.5 percentage points lower than the categorical schemed model. When increasing the translation between images, the networks were predominantly affected once the translation reached a fourth of the image. Our work concludes that architectures designed to cluster data have an advantage when designing an authentication system based on neural networks.
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| 4. |
- Lillie, Mette, et al.
(författare)
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Contrasting segregation patterns among endogenous retroviruses across the koala population
- 2024
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Ingår i: Communications Biology. - : Springer Nature. - 2399-3642. ; 7:1
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Tidskriftsartikel (refereegranskat)abstract
- Koalas (Phascolarctos cinereus) have experienced a history of retroviral epidemics leaving their trace as heritable endogenous retroviruses (ERVs) in their genomes. A recently identified ERV lineage, named phaCin-β, shows a pattern of recent, possibly current, activity with high insertional polymorphism in the population. Here, we investigate geographic patterns of three focal ERV lineages of increasing estimated ages, from the koala retrovirus (KoRV) to phaCin-β and to phaCin-β-like, using the whole-genome sequencing of 430 koalas from the Koala Genome Survey. Thousands of ERV loci were found across the population, with contrasting patterns of polymorphism. Northern individuals had thousands of KoRV integrations and hundreds of phaCin-β ERVs. In contrast, southern individuals had higher phaCin-β frequencies, possibly reflecting more recent activity and a founder effect. Overall, our findings suggest high ERV burden in koalas, reflecting historic retrovirus-host interactions. Importantly, the ERV catalogue supplies improved markers for conservation genetics in this endangered species.
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| 5. |
- Mihalič, Filip, et al.
(författare)
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Conservation of Affinity Rather Than Sequence Underlies a Dynamic Evolution of the Motif-Mediated p53/MDM2 Interaction in Ray-Finned Fishes
- 2024
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Ingår i: Molecular biology and evolution. - : Oxford University Press. - 0737-4038 .- 1537-1719. ; 41:2
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Tidskriftsartikel (refereegranskat)abstract
- The transcription factor and cell cycle regulator p53 is marked for degradation by the ubiquitin ligase MDM2. The interaction between these 2 proteins is mediated by a conserved binding motif in the disordered p53 transactivation domain (p53TAD) and the folded SWIB domain in MDM2. The conserved motif in p53TAD from zebrafish displays a 20-fold weaker interaction with MDM2, compared to the interaction in human and chicken. To investigate this apparent difference, we tracked the molecular evolution of the p53TAD/MDM2 interaction among ray-finned fishes (Actinopterygii), the largest vertebrate clade. Intriguingly, phylogenetic analyses, ancestral sequence reconstructions, and binding experiments showed that different loss-of-affinity changes in the canonical binding motif within p53TAD have occurred repeatedly and convergently in different fish lineages, resulting in relatively low extant affinities (KD = 0.5 to 5 mu M). However, for 11 different fish p53TAD/MDM2 interactions, nonconserved regions flanking the canonical motif increased the affinity 4- to 73-fold to be on par with the human interaction. Our findings suggest that compensating changes at conserved and nonconserved positions within the motif, as well as in flanking regions of low conservation, underlie a stabilizing selection of "functional affinity" in the p53TAD/MDM2 interaction. Such interplay complicates bioinformatic prediction of binding and calls for experimental validation. Motif-mediated protein-protein interactions involving short binding motifs and folded interaction domains are very common across multicellular life. It is likely that the evolution of affinity in motif-mediated interactions often involves an interplay between specific interactions made by conserved motif residues and nonspecific interactions by nonconserved disordered regions.
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| 6. |
- Mohamadnejad Sangdehi, Fahime, et al.
(författare)
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Copy number variation and elevated genetic diversity at immune trait loci in Atlantic and Pacific herring
- 2024
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Ingår i: BMC Genomics. - : BioMed Central (BMC). - 1471-2164. ; 25:1
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundGenome-wide comparisons of populations are widely used to explore the patterns of nucleotide diversity and sequence divergence to provide knowledge on how natural selection and genetic drift affect the genome. In this study we have compared whole-genome sequencing data from Atlantic and Pacific herring, two sister species that diverged about 2 million years ago, to explore the pattern of genetic differentiation between the two species.ResultsThe genome comparison of the two species revealed high genome-wide differentiation but with islands of remarkably low genetic differentiation, as measured by an FST analysis. However, the low FST observed in these islands is not caused by low interspecies sequence divergence (dxy) but rather by exceptionally high estimated intraspecies nucleotide diversity (π). These regions of low differentiation and elevated nucleotide diversity, termed high-diversity regions in this study, are not enriched for repeats but are highly enriched for immune-related genes. This enrichment includes genes from both the adaptive immune system, such as immunoglobulin, T-cell receptor and major histocompatibility complex genes, as well as a substantial number of genes with a role in the innate immune system, e.g. novel immune-type receptor, tripartite motif and tumor necrosis factor receptor genes. Analysis of long-read based assemblies from two Atlantic herring individuals revealed extensive copy number variation in these genomic regions, indicating that the elevated intraspecies nucleotide diversities were partially due to the cross-mapping of short reads.ConclusionsThis study demonstrates that copy number variation is a characteristic feature of immune trait loci in herring. Another important implication is that these loci are blind spots in classical genome-wide screens for genetic differentiation using short-read data, not only in herring, likely also in other species harboring qualitatively similar variation at immune trait loci. These loci stood out in this study because of the relatively high genome-wide baseline for FST values between Atlantic and Pacific herring.
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| 7. |
- Pettersson, Mats, et al.
(författare)
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Limited Parallelism in Genetic Adaptation to Brackish Water Bodies in European Sprat and Atlantic Herring
- 2024
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Ingår i: Genome Biology and Evolution. - : Oxford University Press. - 1759-6653. ; 16:7
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Tidskriftsartikel (refereegranskat)abstract
- The European sprat is a small plankton-feeding clupeid present in the northeastern Atlantic Ocean, in the Mediterranean Sea, and in the brackish Baltic Sea and Black Sea. This species is the target of a major fishery and, therefore, an accurate characterization of its genetic population structure is crucial to delineate proper stock assessments that aid ensuring the fishery's sustainability. Here, we present (i) a draft genome assembly, (ii) pooled whole genome sequencing of 19 population samples covering most of the species' distribution range, and (iii) the design and test of a single nucleotide polymorphism (SNP)-chip resource and use this to validate the population structure inferred from pooled sequencing. These approaches revealed, using the populations sampled here, three major groups of European sprat: Oceanic, Coastal, and Brackish with limited differentiation within groups even over wide geographical stretches. Genetic structure is largely driven by six large putative inversions that differentiate Oceanic and Brackish sprats, while Coastal populations display intermediate frequencies of haplotypes at each locus. Interestingly, populations from the Baltic and the Black Seas share similar frequencies of haplotypes at these putative inversions despite their distant geographic location. The closely related clupeids European sprat and Atlantic herring both show genetic adaptation to the brackish Baltic Sea, providing an opportunity to explore the extent of genetic parallelism. This analysis revealed limited parallelism because out of 125 independent loci detected in the Atlantic herring, three showed sharp signals of selection that overlapped between the two species and contained single genes such as PRLRA, which encodes the receptor for prolactin, a freshwater-adapting hormone in euryhaline species, and THRB, a receptor for thyroid hormones, important both for metabolic regulation and the development of red cone photoreceptors.
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| 8. |
- Ramos, Lucas P., et al.
(författare)
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Change Detection in Wavelength-Resolution SAR Image Stack Based on Tensor Robust PCA
- 2024
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Ingår i: IEEE Geoscience and Remote Sensing Letters. - : Institute of Electrical and Electronics Engineers (IEEE). - 1545-598X .- 1558-0571. ; 21
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Tidskriftsartikel (refereegranskat)abstract
- Wavelength-resolution (WR) synthetic aperture radar (SAR) change detection (CD) has been used to detect concealed targets in forestry areas. However, most proposed methods are generally based on matrix or vector analyses and, therefore, do not exploit information embedded in multidimensional data. In this letter, a CD method for WR SAR image stacks based on tensor robust principal component analysis (TRPCA) is proposed. The proposed CD method used the new tensor nuclear norm induced by the definition of the tensor-tensor product to exploit temporal and spatial information contained in the image stack. To assess the performance of the proposed method, we considered SAR images obtained by the very high frequency (VHF) WR CARABAS-II SAR system. Experiments for three different stack sizes show that a significant performance gain can be achieved when large image stacks are considered. The proposed CD method performs better in terms of probability of detection (PD) and false alarm rate (FAR) than the other five CD methods in VHF WR SAR images, including one based on matrix robust principal component analysis (RPCA). In a particular setting, it achieves a PD of 99% and a FAR of 0.028 false alarms per km2. Authors
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| 9. |
- Vu, Viet Thuy, 1977-, et al.
(författare)
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3D Hyper-accurate Localization in Indoor Environment for Mobile Equipment
- 2024
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Ingår i: ICCE 2024 - 2024 IEEE 10th International Conference on Communications and Electronics. - : Institute of Electrical and Electronics Engineers (IEEE). - 9798350379785 ; , s. 706-711
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Konferensbidrag (refereegranskat)abstract
- A solution for the three-dimensional (3D) hyper-accurate localization in indoor environment for mobile equipment problem can be based on radar systems. Mobile equipment with an integrated radar system is known as a joint radar-communication (JRC) system or a joint communication and sensing (JCAS) system. The paper proposes an approach for 3D hyper-accurate localization in indoor environment without modifications of cellular network infrastructure. The simulations and experiments show the feasibility of the proposal. © 2024 IEEE.
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| 10. |
- Alves, Dimas irion, et al.
(författare)
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Change Detection Method for Wavelength-Resolution SAR Images Based on Bayes’ Theorem : An Iterative Approach
- 2023
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Ingår i: IEEE Access. - Piscataway, NJ : Institute of Electrical and Electronics Engineers (IEEE). - 2169-3536. ; 11, s. 84734-84743
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Tidskriftsartikel (refereegranskat)abstract
- This paper presents an iterative change detection (CD) method based on Bayes’ theorem for very high-frequency (VHF) ultra-wideband (UWB) SAR images considering commonly used clutter-plus-noise statistical models. The proposed detection technique uses the information of the detected changes to iteratively update the data and distribution information, obtaining more accurate clutter-plus-noise statistics resulting in false alarm reduction. The Bivariate Rayleigh and Bivariate Gaussian distributions are investigated as candidates to model the clutter-plus-noise, and the Anderson-Darling goodness-of-fit test is used to investigate three scenarios of interest. Different aspects related to the distributions are discussed, the observed mismatches are analyzed, and the impact of the distribution chosen for the proposed iterative change detection method is analyzed. Finally, the proposed iterative method performance is assessed in terms of the probability of detection and false alarm rate and compared with other competitive solutions. The experimental evaluation uses data from real measurements obtained using the CARABAS II SAR system. Results show that the proposed iterative CD algorithm performs better than the other methods. Author
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