| 1. |
- Hudson, Lawrence N, et al.
(författare)
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The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project
- 2017
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Ingår i: Ecology and Evolution. - : John Wiley & Sons. - 2045-7758. ; 7:1, s. 145-188
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Tidskriftsartikel (refereegranskat)abstract
- The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.
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| 2. |
- Han, Sang Sub, et al.
(författare)
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Peel-and-Stick Integration of Atomically Thin Nonlayered PtS Semiconductors for Multidimensionally Stretchable Electronic Devices
- 2022
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Ingår i: ACS Applied Materials and Interfaces. - : American Chemical Society (ACS). - 1944-8244 .- 1944-8252. ; 14:17, s. 20268-20279
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Tidskriftsartikel (refereegranskat)abstract
- van der Waals (vdW) crystals with unparalleled electromechanical properties have been explored for transformative devices. Currently, the availability of 2D vdW crystals is rather limited in nature as they are only obtained from certain mother crystals with intrinsically possessed layered crystallinity and anisotropic molecular bonding. Recent efforts to transform conventionally non-vdW three-dimensional (3D) crystals into ultrathin 2D-like structures have seen rapid developments to explore device building blocks of unique form factors. Herein, we explore a "peel-and-stick" approach, where a nonlayered 3D platinum sulfide (PtS) crystal, traditionally known as a cooperate mineral material, is transformed into a freestanding 2D-like membrane for electromechanical applications. The ultrathin (???10 nm) 3D PtS films grown on large-area (>cm2) silicon dioxide/silicon (SiO2/Si) wafers are precisely "peeled" inside water retaining desired geometries via a capillary-force-driven surface wettability control. Subsequently, they are "sticked" on strain-engineered patterned substrates presenting prominent semiconducting properties, i.e., p-type transport with an optical band gap of ∼1.24 eV. A variety of mechanically deformable strain-invariant electronic devices have been demonstrated by this peel-and-stick method, including biaxially stretchable photodetectors and respiratory sensing face masks. This study offers new opportunities of 2D-like nonlayered semiconducting crystals for emerging mechanically reconfigurable and stretchable device technologies.
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| 3. |
- Macpherson, Alex, et al.
(författare)
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The allosteric modulation of complement C5 by knob domain peptides
- 2021
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Ingår i: eLIFE. - : ELife Sciences Publications Ltd. - 2050-084X. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Bovines have evolved a subset of antibodies with ultra-long heavy chain complementarity determining regions that harbour cysteine-rich knob domains. To produce high-affinity peptides, we previously isolated autonomous 3-6 kDa knob domains from bovine antibodies. Here, we show that binding of four knob domain peptides elicits a range of effects on the clinically validated drug target complement C5. Allosteric mechanisms predominated, with one peptide selectively inhibiting C5 cleavage by the alternative pathway C5 convertase, revealing a targetable mechanistic difference between the classical and alternative pathway C5 convertases. Taking a hybrid biophysical approach, we present C5-knob domain co-crystal structures and, by solution methods, observed allosteric effects propagating >50 angstrom from the binding sites. This study expands the therapeutic scope of C5, presents new inhibitors, and introduces knob domains as new, low molecular weight antibody fragments, with therapeutic potential.
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| 4. |
- Chatzimparmpas, Angelos
(författare)
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Visual Analytics for Explainable and Trustworthy Machine Learning
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The deployment of artificial intelligence solutions and machine learning research has exploded in popularity in recent years, with numerous types of models proposed to interpret and predict patterns and trends in data from diverse disciplines. However, as the complexity of these models grows, it becomes increasingly difficult for users to evaluate and rely on the model results, since their inner workings are mostly hidden in black boxes, which are difficult to trust in critical decision-making scenarios. While automated methods can partly handle these problems, recent research findings suggest that their combination with innovative methods developed within information visualization and visual analytics can lead to further insights gained from models and, consequently, improve their predictive ability and enhance trustworthiness in the entire process. Visual analytics is the area of research that studies the analysis of vast and intricate information spaces by combining statistical and machine learning models with interactive visual interfaces. By following this methodology, human experts can better understand such spaces and apply their domain expertise in the process of building and improving the underlying models.The primary goals of this dissertation are twofold, focusing on (1) methodological aspects, by conducting qualitative and quantitative meta-analyses to support the visualization research community in making sense of its literature and to highlight unsolved challenges, as well as (2) technical solutions, by developing visual analytics approaches for various machine learning models, such as dimensionality reduction and ensemble learning methods. Regarding the first goal, we define, categorize, and examine in depth the means for visual coverage of the different trust levels at each stage of a typical machine learning pipeline and establish a design space for novel visualizations in the area. Regarding the second goal, we discuss multiple visual analytics tools and systems implemented by us to facilitate the underlying research on the various stages of the machine learning pipeline, i.e., data processing, feature engineering, hyperparameter tuning, understanding, debugging, refining, and comparing models. Our approaches are data-agnostic, but mainly target tabular data with meaningful attributes in diverse domains, such as health care and finance. The applicability and effectiveness of this work were validated with case studies, usage scenarios, expert interviews, user studies, and critical discussions of limitations and alternative designs. The results of this dissertation provide new avenues for visual analytics research in explainable and trustworthy machine learning.
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| 5. |
- Fagerqvist, Therese, et al.
(författare)
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Monoclonal antibodies selective for α-synuclein oligomers/protofibrils recognize brain pathology in Lewy body disorders and α-synuclein transgenic mice with the disease-causing A30P mutation
- 2013
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Ingår i: Journal of Neurochemistry. - : Wiley-Blackwell. - 0022-3042 .- 1471-4159. ; 126:1, s. 131-144
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Tidskriftsartikel (refereegranskat)abstract
- Inclusions of intraneuronal alpha-synuclein (-synuclein) can be detected in brains of patients with Parkinson's disease and dementia with Lewy bodies. The aggregation of -synuclein is a central feature of the disease pathogenesis. Among the different -synuclein species, large oligomers/protofibrils have particular neurotoxic properties and should therefore be suitable as both therapeutic and diagnostic targets. Two monoclonal antibodies, mAb38F and mAb38E2, with high affinity and strong selectivity for large -synuclein oligomers were generated. These antibodies, which do not bind amyloid-beta or tau, recognize Lewy body pathology in brains from patients with Parkinson's disease and dementia with Lewy bodies and detect pathology earlier in -synuclein transgenic mice than linear epitope antibodies. An oligomer-selective sandwich ELISA, based on mAb38F, was set up to analyze brain extracts of the transgenic mice. The overall levels of -synuclein oligomers/protofibrils were found to increase with age in these mice, although the levels displayed a large interindividual variation. Upon subcellular fractionation, higher levels of -synuclein oligomers/protofibrils could be detected in the endoplasmic reticulum around the age when behavioral disturbances develop. In summary, our novel oligomer-selective -synuclein antibodies recognize relevant pathology and should be important tools to further explore the pathogenic mechanisms in Lewy body disorders. Moreover, they could be potential candidates both for immunotherapy and as reagents in an assay to assess a potential disease biomarker.
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| 6. |
- Fagerqvist, Therese, et al.
(författare)
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Off-pathway α-synuclein oligomers seem to alter α-synuclein turnover in a cell model but lack seeding capability in vivo
- 2013
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Ingår i: Amyloid. - : Informa Healthcare. - 1350-6129 .- 1744-2818. ; 20:4, s. 233-244
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Tidskriftsartikel (refereegranskat)abstract
- Aggregated alpha-synuclein is the major component of Lewy bodies, protein inclusions observed in the brain in neurodegenerative disorders such as Parkinson's disease and dementia with Lewy bodies. Experimental evidence indicates that alpha-synuclein potentially can be transferred between cells and act as a seed to accelerate the aggregation process. Here, we investigated in vitro and in vivo seeding effects of alpha-synuclein oligomers induced by the reactive aldehyde 4-oxo-2-nonenal (ONE). As measured by a Thioflavin-T based fibrillization assay, there was an earlier onset of aggregation when alpha-synuclein oligomers were added to monomeric alpha-synuclein. In contrast, exogenously added alpha-synuclein oligomers did not induce aggregation in a cell model. However, cells overexpressing alpha-synuclein that were treated with the oligomers displayed reduced alpha-synuclein levels, indicating that internalized oligomers either decreased the expression or accelerated the degradation of transfected alpha-synuclein. Also in vivo there were no clear seeding effects, as intracerebral injections of alpha-synuclein oligomers into the neocortex of alpha-synuclein transgenic mice did not induce formation of proteinase K resistant alpha-synuclein pathology. Taken together, we could observe a seeding effect of the ONE-induced alpha-synuclein oligomers in a fibrillization assay, but neither in a cell nor in a mouse model.
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| 7. |
- Han, Sang Sub, et al.
(författare)
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Reversible Transition of Semiconducting PtSe2 and Metallic PtTe2 for Scalable All-2D Edge-Contacted FETs
- 2024
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Ingår i: Nano Letters. - : American Chemical Society (ACS). - 1530-6984 .- 1530-6992. ; 24:6, s. 1891-1900
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Tidskriftsartikel (refereegranskat)abstract
- Two-dimensional (2D) transition metal dichalcogenide (TMD) layers are highly promising as field-effect transistor (FET) channels in the atomic-scale limit. However, accomplishing this superiority in scaled-up FETs remains challenging due to their van der Waals (vdW) bonding nature with respect to conventional metal electrodes. Herein, we report a scalable approach to fabricate centimeter-scale all-2D FET arrays of platinum diselenide (PtSe2) with in-plane platinum ditelluride (PtTe2) edge contacts, mitigating the aforementioned challenges. We realized a reversible transition between semiconducting PtSe2 and metallic PtTe2 via a low-temperature anion exchange reaction compatible with the back-end-of-line (BEOL) processes. All-2D PtSe2 FETs seamlessly edge-contacted with transited metallic PtTe2 exhibited significant performance improvements compared to those with surface-contacted gold electrodes, e.g., an increase of carrier mobility and on/off ratio by over an order of magnitude, achieving a maximum hole mobility of similar to 50.30 cm(2) V-1 s(-1) at room temperature. This study opens up new opportunities toward atomically thin 2D-TMD-based circuitries with extraordinary functionalities.
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| 8. |
- Nilsson, Per H., 1980-, et al.
(författare)
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A Conformational Change of Complement C5 Is Required for Thrombin-Mediated Cleavage, Revealed by a Novel Ex Vivo Human Whole Blood Model Preserving Full Thrombin Activity
- 2021
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Ingår i: Journal of Immunology. - : American Association of Immunologists. - 0022-1767 .- 1550-6606. ; 207:6, s. 1641-1651
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Tidskriftsartikel (refereegranskat)abstract
- Thrombin activation of C5 connects thrombosis to inflammation. Complement research in whole blood ex vivo necessitates anticoagulation, which potentially interferes with the inflammatory modulation by thrombin. We challenged the concept of thrombin as an activator of native C5 by analyzing complement activation and C5 cleavage in human whole blood anticoagulated with Gly-Pro-Arg-Pro (GPRP), a peptide targeting fibrin polymerization downstream of thrombin, allowing complete endogenous thrombin generation. GPRP dose-dependently inhibited coagulation but allowed for platelet activation in accordance with thrombin generation. Spontaneous and bacterial-induced complement activation by Escherichia coli and Staphylococcus aureus, analyzed at the level of C3 and C5, were similar in blood anticoagulated with GPRP and the thrombin inhibitor lepirudin. In the GPRP model, endogenous thrombin, even at supra-physiologic concentrations, did not cleave native C5, despite efficiently cleaving commercially sourced purified C5 protein, both in buffer and when added to C5-deficient serum. In normal serum, only exogenously added, commercially sourced C5 was cleaved, whereas the native plasma C5 remained intact. Crucially, affinity-purified C5, eluted under mild conditions using an MgCl2 solution, was not cleaved by thrombin. Acidification of plasma to pH # 6.8 by hydrochloric or lactic acid induced a C5 antigenic change, nonreversible by pH neutralization, that permitted cleavage by thrombin. Circular dichroism on purified C5 confirmed the structural change during acidification. Thus, we propose that pH-induced conformational change allows thrombin-mediated cleavage of C5 and that, contrary to previous reports, thrombin does not cleave plasma C5 in its native form, suggesting that thrombin cleavage of C5 may be restricted to certain pathophysiological conditions.
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