| 1. |
- Chang, Qi, et al.
(författare)
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DeepRecon : Joint 2D Cardiac Segmentation and 3D Volume Reconstruction via a Structure-Specific Generative Method
- 2022
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Ingår i: Medical Image Computing and Computer Assisted Intervention – MICCAI 2022 - 25th International Conference, Proceedings. - Cham : Springer Nature Switzerland. - 0302-9743 .- 1611-3349. - 9783031164392 ; 13434 LNCS, s. 567-577
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Konferensbidrag (refereegranskat)abstract
- Joint 2D cardiac segmentation and 3D volume reconstruction are fundamental in building statistical cardiac anatomy models and understanding functional mechanisms from motion patterns. However, due to the low through-plane resolution of cine MR and high inter-subject variance, accurately segmenting cardiac images and reconstructing the 3D volume are challenging. In this study, we propose an end-to-end latent-space-based framework, DeepRecon, that generates multiple clinically essential outcomes, including accurate image segmentation, synthetic high-resolution 3D image, and 3D reconstructed volume. Our method identifies the optimal latent representation of the cine image that contains accurate semantic information for cardiac structures. In particular, our model jointly generates synthetic images with accurate semantic information and segmentation of the cardiac structures using the optimal latent representation. We further explore downstream applications of 3D shape reconstruction and 4D motion pattern adaptation by the different latent-space manipulation strategies. The simultaneously generated high-resolution images present a high interpretable value to assess the cardiac shape and motion. Experimental results demonstrate the effectiveness of our approach on multiple fronts including 2D segmentation, 3D reconstruction, downstream 4D motion pattern adaption performance.
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| 2. |
- Bhat, Goutam, et al.
(författare)
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NTIRE 2022 Burst Super-Resolution Challenge
- 2022
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Ingår i: 2022 IEEE/CVF CONFERENCE ON COMPUTER VISION AND PATTERN RECOGNITION WORKSHOPS (CVPRW 2022). - : IEEE. - 9781665487399 - 9781665487405 ; , s. 1040-1060
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Konferensbidrag (refereegranskat)abstract
- Burst super-resolution has received increased attention in recent years due to its applications in mobile photography. By merging information from multiple shifted images of a scene, burst super-resolution aims to recover details which otherwise cannot be obtained using a simple input image. This paper reviews the NTIRE 2022 challenge on burst super-resolution. In the challenge, the participants were tasked with generating a clean RGB image with 4x higher resolution, given a RAW noisy burst as input. That is, the methods need to perform joint denoising, demosaicking, and super-resolution. The challenge consisted of 2 tracks. Track 1 employed synthetic data, where pixel-accurate high-resolution ground truths are available. Track 2 on the other hand used real-world bursts captured from a handheld camera, along with approximately aligned reference images captured using a DSLR. 14 teams participated in the final testing phase. The top performing methods establish a new state-of-the-art on the burst super-resolution task.
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| 3. |
- Delios, A., et al.
(författare)
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Examining the generalizability of research findings from archival data
- 2022
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 119:30
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Tidskriftsartikel (refereegranskat)abstract
- This initiative examined systematically the extent to which a large set of archival research findings generalizes across contexts. We repeated the key analyses for 29 original strategic management effects in the same context (direct reproduction) as well as in 52 novel time periods and geographies; 45% of the reproductions returned results matching the original reports together with 55% of tests in different spans of years and 40% of tests in novel geographies. Some original findings were associated with multiple new tests. Reproducibility was the best predictor of generalizability-for the findings that proved directly reproducible, 84% emerged in other available time periods and 57% emerged in other geographies. Overall, only limited empirical evidence emerged for context sensitivity. In a forecasting survey, independent scientists were able to anticipate which effects would find support in tests in new samples.
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| 4. |
- Gehrmann, Sebastian, et al.
(författare)
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GEMv2: Multilingual NLG Benchmarking in a Single Line of Code
- 2022
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Ingår i: Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing: System Demonstrations. - : Association for Computational Linguistics (ACL). ; , s. 266-281
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Konferensbidrag (refereegranskat)abstract
- Evaluations in machine learning rarely use the latest metrics, datasets, or human evaluation in favor of remaining compatible with prior work. The compatibility, often facilitated through leaderboards, thus leads to outdated but standardized evaluation practices. We pose that the standardization is taking place in the wrong spot. Evaluation infrastructure should enable researchers to use the latest methods and what should be standardized instead is how to incorporate these new evaluation advances.We introduce GEMv2, the new version of the Generation, Evaluation, and Metrics Benchmark which uses a modular infrastructure for dataset, model, and metric developers to benefit from each other’s work. GEMv2 supports 40 documented datasets in 51 languages, ongoing online evaluation for all datasets, and our interactive tools make it easier to add new datasets to the living benchmark.
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| 5. |
- Jiang, Kun
(författare)
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Modulating the structure-function relationship of mucin materials
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Mucus covers the epithelium surfaces playing a key role in the barrier, hydration, lubrication and bioactivity functions for the human body, and mucins are the fundamental components of mucus which provide such functions. However, many details in how these functions are related to the many structural features of mucins are still unknown. In this thesis, strategies were developed to modify mucin structures in defined ways to gain insights and controls over several key functions of this molecule. We altered functional motifs on the mucin molecules, and changed the conformation of mucin networks to modulate the accessibility of such functional motifs. Then functional outcomes, including macrophage responses, diffusion of molecules through mucin networks, and mucin lubricity were studied. This thesis is organized into three parts according to the three functions. We found that the responses of macrophage to mucins were modulated by changing the location of crosslinks between mucins and by the immobilization of mucins onto surfaces. Mucins’ bottle-brush structure allowed their crosslinking either via the protein backbone or via the glycan side chains with similar crosslinking density. With the same crosslinking structure, the placement of mucin thin film on hard substrate and soft substrate led to different macrophage responses, and only mucin coating on soft gel induced similar immune responses as that of mucin gels. A better understanding of how mucin bioactivity, and specifically immune-modulating properties, can be modulated, provide new strategies to develop biomaterials with defined bioactivities. This work could also inspire innovative treatments to modulate mucin bioactivities in vivo to treat mucin-related diseases such as for mucinous cancers. The diffusion of molecules through mucin gels was modulated by changing the gel network and their affinity filtration capacity. By locating the crosslinking sites on the protein backbone or the glycan chains, the gel network remained the same with similar diffusion profiles of dextrans. However, with simple change of mucin concentration, molecules of different size diffused faster in gels with lower mucin concentration. The affinity filtration of mucin gel was modulated by removing sialic acids, which acts as binding sites for molecules or cells via electrostatic interactions or specific binding, and the binding can slow down diffusion of cells or molecules. By altering sialic acid contents, the diffusion of charged dextran was modulated and the penetration of sperms was increased. With the understanding, mucin gels with controlled permeability can be designed for loading drugs or encapsulating tissue. And strategies can be developed in the future for treating mucus barrier related disease in vivo, such as inflammatory bowel disease.The hydration & lubrication of mucin coating was modulated with changed mucin structure and removal of associated impurities. The hydration of mucin coatings remained the same, but their lubricity was lost by removing negatively charged sugars. However, the components associated with mucin, such as DNA, compensated for the missing of negative sugars. Commercial PGM was found with damaged glycosylation and missing peptide domains, and its lubricity was lost completely compared to lab-purified mucins. With this knowledge, mucin structure can be modulated for desired hydration and lubrication performance, and this can inspire to develop strategies for restoring their hydration and lubricity in vivo during diseases, such as dry eye.
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| 6. |
- Kanoni, Stavroula, et al.
(författare)
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Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis.
- 2022
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Ingår i: Genome biology. - : Springer Science and Business Media LLC. - 1474-760X .- 1465-6906 .- 1474-7596. ; 23:1
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Tidskriftsartikel (refereegranskat)abstract
- Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery.To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N=1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3-5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism.Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk.
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| 7. |
- Koskela, Salla, et al.
(författare)
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Hemicellulose content affects the properties of cellulose nanofibrils produced from softwood pulp fibres by LPMO
- 2022
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Ingår i: Green Chemistry. - : Royal Society of Chemistry (RSC). - 1463-9262 .- 1463-9270.
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Tidskriftsartikel (refereegranskat)abstract
- Lytic polysaccharide monooxygenase (LPMO)-catalysed oxidation of cellulose has emerged as a green alternative to chemical modifications in the production of cellulose nanofibrils (CNFs) from wood pulp fibres. The effect of the hemicellulose content of the starting pulp fibres on the oxidation capabilities of cellulose-active LPMO is important and has not been investigated previously. In this study, the production of LPMO-oxidised CNFs was evaluated on two commercial softwood pulp fibres with different hemicellulose contents. Thin and colloidally stable CNFs were readily obtained from kraft pulp with a hemicellulose content of 16%. The preserved hemicellulose fraction in the kraft pulp enhanced the access of LPMO into the fibre cell wall, enabling the production of homogeneous CNFs with a thin width of 3.7 ± 1.7 nm. By contrast, the LPMO-oxidised dissolving pulp with a lower hemicellulose content of 4% could only be partially disintegrated into thin CNFs, leaving a large amount of cellulose microfibril aggregates with widths of around 50 to 100 nm. CNFs disintegrated from the LPMO-oxidised kraft pulp could be processed into nanopapers with excellent properties including an optical transmittance of 86%, tensile strength of 260 MPa, and Young's modulus of 16.9 GPa. Such CNFs also showed acid-triggered nanofibril gelation owing to the introduced carboxyl groups on cellulose microfibril surfaces. These results indicate that the inherent hemicelluloses present in the wood cell wall are essential for LPMO-mediated CNF production from wood pulp fibres.
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| 8. |
- Koskela, Salla, 1990-
(författare)
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Lytic polysaccharide monooxygenases for green production of cellulose nanomaterials
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Cellulose is the main structural polymer in wood, and its potential in the form of nanomaterial building blocks, nanocelluloses, has now been recognized. Nanocelluloses, including cellulose nanofibers (CNFs) and cellulose nanocrystals (CNCs), have become increasingly important in development of modern sustainable materials. Nanocelluloses are typically produced from wood pulp fibers by chemical pre-treatments that deposit charged functional groups onto cellulose microfibril surfaces, thereby promoting disintegration of the fiber cell wall during mechanical fibrillation. Due to environmental risks related to the use of harsh chemical treatments, it is crucial to develop greener, nature-inspired alternatives. As renowned decomposers of wood, fungi secrete cellulose-active enzymes that work in aqueous reaction conditions. Of these, lytic polysaccharide monooxygenases (LPMOs) have piqued a special interest in green production of nanocellulose owing to their ability to introduce charged carboxyl groups onto cellulose surfaces. However, little is known about the properties of LPMO-oxidized nanocelluloses, their mechanical performance in bulk materials, and the mechanism how LPMOs facilitate fibrillation of the wood fiber cells.This PhD thesis aimed to dissect the potential of C1-oxidizing LPMOs in the production of nanocelluloses and to clarify the mechanism of LPMO oxidation that facilitates the disintegration of wood cell wall. LPMOs with and without attached carbohydrate-binding modules (CBMs) were recombinantly produced in Pichia pastoris and studied for the production of CNFs and CNCs, which were further processed into bulk materials. The morphology and properties of the nanocelluloses, and the optical and mechanical properties of the bulk materials were characterized. In addition, delignified wood with a preserved cellular structure was used as a model substrate for LPMO oxidation, and the LPMO-induced changes in the wood cell wall structure were investigated using advanced scattering techniques.The results on CNF production showed that LPMO-oxidized wood pulp fibers can be transformed into discrete and colloidal CNFs by mild mechanical disintegration, analogous to chemical pre-treatments such as 2,2,6,6-tetramethylpyperidine-1-oxy radical (TEMPO)-mediated oxidation. Importantly, these CNFs were well individualized with an average width of 4 nm, resembling that of cellulose microfibrils in wood. Such CNFs were obtained from softwood holocellulose- and kraft pulp fibers with a hemicellulose content of 16–19%, but not from dissolving pulp with a lower hemicellulose content of 4%. Nanopapers prepared from the LPMO-oxidized CNFs were transparent and they demonstrated tensile strengths of ca. 260 MPa and Young’s moduli of ca. 17 GPa. The water suspensions of LPMO-oxidized CNFs also exhibited acid-triggered gelation behavior due to the enzymatically introduced carboxyl groups.LPMO oxidation was also found applicable in the preparation of CNCs from microcrystalline cellulose. The LPMO-oxidized CNCs had a needle-like morphology and they formed stable colloidal suspensions in water that demonstrated flow-induced birefringence. Solution cast films showed that the CNCs bearing C1 carboxyl groups possessed the pivotal ability to undergo self-assembly into an anisotropic phase. As some LPMOs are appended to a non-catalytic CBM, the effect of this module on nanocellulose production was also determined. CBM was found to increase the release of carboxyl groups from cellulose microfibril surfaces in the form of soluble cello-oligosaccharides. By contrast, a non-modular LPMO introduced more carboxyl groups to the cellulose surfaces, up to 0.53 mmol g-1 on CNFs, and 0.70 mmol g-1 on CNCs. Indeed, a non-modular LPMO was found advantageous in production of both CNFs and CNCs.Despite the important role of LPMOs for natural and biotechnological degradation of wood biomass, the LPMO-induced changes in the wood cell wall structure have remained unknown. In this work, these changes were characterized for the first time. It was shown that a C1-oxiding LPMO can modulate cellulose microfibrils and disrupt the wood cell wall ultrastructure by modifying cellulose surface chemistry. After the LPMO oxidation, the average distance between cellulose microfibril centers increased from 4.1 nm to 10.7 nm, signifying the separation of microfibrils in a microfibril bundle. This result revealed a previously unidentified role for C1-oxidizing LPMOs in degradation of cellulose at the nanoscale. Remarkably, LPMO-treated wood veneers could be further compressed into anisotropic, transparent films with an ultrahigh tensile strength of 824 MPa.In summary, this PhD thesis clarified the potential of C1-oxidizing LPMOs in green production of nanocelluloses and showed that LPMO oxidation is a suitable method to obtain high-performing isotropic and anisotropic bulk materials from wood. On the basis of the obtained findings, a new model was also proposed which elucidates the mechanism of cellulose degradation at the nanoscale. This study broadened the understanding of LPMOs including their biological- and biotechnological significance and provided new insights into the use of LPMOs for the preparation of cellulose-based nanomaterials.
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| 9. |
- Lu, Yang, et al.
(författare)
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Precise tuning of interlayer electronic coupling in layered conductive metal-organic frameworks
- 2022
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Ingår i: Nature Communications. - : Nature Portfolio. - 2041-1723. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Layered metal-organic frameworks attract interests for optoelectronics and spintronics. Here, the authors report a strategy to tune interlayer charge transport and thermoelectric properties via side-chain induced control of the layer spacing. Two-dimensional conjugated metal-organic frameworks (2D c-MOFs) have attracted increasing interests for (opto)-electronics and spintronics. They generally consist of van der Waals stacked layers and exhibit layer-depended electronic properties. While considerable efforts have been made to regulate the charge transport within a layer, precise control of electronic coupling between layers has not yet been achieved. Herein, we report a strategy to precisely tune interlayer charge transport in 2D c-MOFs via side-chain induced control of the layer spacing. We design hexaiminotriindole ligands allowing programmed functionalization with tailored alkyl chains (HATI_CX, X = 1,3,4; X refers to the carbon numbers of the alkyl chains) for the synthesis of semiconducting Ni-3(HATI_CX)(2). The layer spacing of these MOFs can be precisely varied from 3.40 to 3.70 angstrom, leading to widened band gap, suppressed carrier mobilities, and significant improvement of the Seebeck coefficient. With this demonstration, we further achieve a record-high thermoelectric power factor of 68 +/- 3 nW m(-1) K-2 in Ni-3(HATI_C3)(2), superior to the reported holes-dominated MOFs.
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| 10. |
- Qi, Wen, et al.
(författare)
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Multimodal data fusion framework enhanced robot-assisted minimally invasive surgery
- 2022
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Ingår i: Transactions of the Institute of Measurement and Control. - : SAGE Publications. - 0142-3312 .- 1477-0369. ; 44:4, s. 735-743
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Tidskriftsartikel (refereegranskat)abstract
- The generous application of robot-assisted minimally invasive surgery (RAMIS) promotes human-machine interaction (HMI). Identifying various behaviors of doctors can enhance the RAMIS procedure for the redundant robot. It bridges intelligent robot control and activity recognition strategies in the operating room, including hand gestures and human activities. In this paper, to enhance identification in a dynamic situation, we propose a multimodal data fusion framework to provide multiple information for accuracy enhancement. Firstly, a multi-sensors based hardware structure is designed to capture varied data from various devices, including depth camera and smartphone. Furthermore, in different surgical tasks, the robot control mechanism can shift automatically. The experimental results evaluate the efficiency of developing the multimodal framework for RAMIS by comparing it with a single sensor system. Implementing the KUKA LWR4+ in a surgical robot environment indicates that the surgical robot systems can work with medical staff in the future.
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