| 1. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 2. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 3. |
- Anderson, Cynthia M., et al.
(författare)
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Permanent Genetic Resources added to Molecular Ecology Resources Database 1 December 2009-31 January 2010
- 2010
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 10:3, s. 576-579
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Tidskriftsartikel (refereegranskat)abstract
- This article documents the addition of 220 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Allanblackia floribunda, Amblyraja radiata, Bactrocera cucurbitae, Brachycaudus helichrysi, Calopogonium mucunoides, Dissodactylus primitivus, Elodea canadensis, Ephydatia fluviatilis, Galapaganus howdenae howdenae, Hoplostethus atlanticus, Ischnura elegans, Larimichthys polyactis, Opheodrys vernalis, Pelteobagrus fulvidraco, Phragmidium violaceum, Pistacia vera, and Thunnus thynnus. These loci were cross-tested on the following species: Allanblackia gabonensis, Allanblackia stanerana, Neoceratitis cyanescens, Dacus ciliatus, Dacus demmerezi, Bactrocera zonata, Ceratitis capitata, Ceratitis rosa, Ceratits catoirii, Dacus punctatifrons, Ephydatia mulleri, Spongilla lacustris, Geodia cydonium, Axinella sp., Ischnura graellsii, Ischnura ramburii, Ischnura pumilio, Pistacia integerrima and Pistacia terebinthus.
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| 4. |
- Grossmann, Igor, et al.
(författare)
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Insights into the accuracy of social scientists' forecasts of societal change
- 2023
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Ingår i: Nature Human Behaviour. - : Springer Nature. - 2397-3374. ; 7, s. 484-501
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Tidskriftsartikel (refereegranskat)abstract
- How well can social scientists predict societal change, and what processes underlie their predictions? To answer these questions, we ran two forecasting tournaments testing the accuracy of predictions of societal change in domains commonly studied in the social sciences: ideological preferences, political polarization, life satisfaction, sentiment on social media, and gender-career and racial bias. After we provided them with historical trend data on the relevant domain, social scientists submitted pre-registered monthly forecasts for a year (Tournament 1; N = 86 teams and 359 forecasts), with an opportunity to update forecasts on the basis of new data six months later (Tournament 2; N = 120 teams and 546 forecasts). Benchmarking forecasting accuracy revealed that social scientists' forecasts were on average no more accurate than those of simple statistical models (historical means, random walks or linear regressions) or the aggregate forecasts of a sample from the general public (N = 802). However, scientists were more accurate if they had scientific expertise in a prediction domain, were interdisciplinary, used simpler models and based predictions on prior data. How accurate are social scientists in predicting societal change, and what processes underlie their predictions? Grossmann et al. report the findings of two forecasting tournaments. Social scientists' forecasts were on average no more accurate than those of simple statistical models.
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| 5. |
- Svensson, Ulrika S H, et al.
(författare)
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Artemisinin induces omeprazole metabolism in human beings
- 1998
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Ingår i: Clinical Pharmacology and Therapeutics. - 0009-9236 .- 1532-6535. ; 64, s. 160-
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Tidskriftsartikel (refereegranskat)abstract
- Objective: This study investigated whether time-dependent artemisinin pharmacokinetics correlated to CYP3A4 or CYP2C19 activity in vivo. Methods: Artemisinin (two oral doses per day of 250 mg) was given to nine healthy Vietnamese subjects for 7 days (day 1 to day 7), Single 20 mg doses of omeprazole were given orally on day -7, day 1, and day 7, Single doses of artemisinin and omeprazole were given in combination on day 14 after a 6-day washout period. The pharmacokinetics of artemisinin, omeprazole, hydroxyomeprazole, and omeprazole sulfone were evaluated on days -7, 1, 7, and 14, On the same days urine was collected for the determination of 6 beta-hydroxycortisol and cortisol excretion. Results: Areas under plasma concentration-time curves (AUC) for artemisinin and omeprazole decreased on day 7 to 20% (95% confidence intervals, 13%, 28%) and 35% (25%, 46%), respectively, compared with values on day 1, AUC ratios for hydroxyomeprazole/omeprazole increased 2.2-fold (1,7, 2.7) on day 7 compared with values on day 1, Al values were normalized at day 14, There were no significant changes in the omeprazole sulfone/omeprazole ratio or in the 6 beta-hydroxycortisol/cortisol ratio between the study days. In one subject found to have poor CYP2C19 metabolization, the elimination of omeprazole increased after artemisinin exposure, with no change in the hydroxyomeprazole/omeprazole AUC ratio. Conclusion: Artemisinin did not alter CYP3A4 activity, whereas an increase in CYP2C19 activity was observed. The increased elimination of omeprazole in both poor and extensive CYP2C19 metabolizers suggests artemisinin induces both CYP2C19 and another enzyme.
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| 6. |
- Chen, H., et al.
(författare)
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Unprecedented non-hysteretic superelasticity of [001]-oriented NiCoFeGa single crystals
- 2020
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Ingår i: Nature Materials. - : Nature Research. - 1476-1122 .- 1476-4660.
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Tidskriftsartikel (refereegranskat)abstract
- Superelasticity associated with the martensitic transformation has found a broad range of engineering applications1,2. However, the intrinsic hysteresis3 and temperature sensitivity4 of the first-order phase transformation significantly hinder the usage of smart metallic components in many critical areas. Here, we report a large superelasticity up to 15.2% strain in [001]-oriented NiCoFeGa single crystals, exhibiting non-hysteretic mechanical responses, a small temperature dependence and high-energy-storage capability and cyclic stability over a wide temperature and composition range. In situ synchrotron X-ray diffraction measurements show that the superelasticity is correlated with a stress-induced continuous variation of lattice parameter accompanied by structural fluctuation. Neutron diffraction and electron microscopy observations reveal an unprecedented microstructure consisting of atomic-level entanglement of ordered and disordered crystal structures, which can be manipulated to tune the superelasticity. The discovery of the large elasticity related to the entangled structure paves the way for exploiting elastic strain engineering and development of related functional materials.
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| 7. |
- Cong, D. Y., et al.
(författare)
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Neutron diffraction study on crystal structure and phase transformation in Ni-Mn-Ga ferromagnetic shape memory alloys
- 2007
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Ingår i: Powder Diffraction. - : Cambridge University Press (CUP). - 0885-7156 .- 1945-7413. ; 22:4, s. 307-311
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Tidskriftsartikel (refereegranskat)abstract
- Crystal structure and phase transformation behaviors in two Ni-Mn-Ga ferromagnetic shape memory alloys (FSMAs) with compositions of Ni48Mn30Ga22 and Ni53Mn25Ga22 (at. %) as a function of temperature were investigated by in situ neutron diffraction experiments. Neutron diffraction technique proves to be highly efficient in characterizing structural transformation in Ni-Mn-Ga FSMAs, which consist of nearby elements in the periodic table. Our neutron results show that Ni48Mn30Ga22 has a cubic, L-21 Heusler structure from 373 to 293 K. Its crystal structure changes into a seven-layered orthorhombic martensitic structure when cooled to 243 K, and no further transformation is observed upon cooling to 19 K. Neutron diffraction results also show that Ni53Mn25Ga22 has a tetragonal 14/mmm martensitic structure from 20 to 403 K. A pre-transformation around room temperature is observed from an abrupt jump in unit-cell volume of Ni53Mn25Ga22, which corresponds with an endothermic peak detected in a heated DSC curve.
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| 8. |
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| 9. |
- Peng, Ru, 1960-, et al.
(författare)
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Crystal structure and phase transformation in Ni53Mn 25Ga22 shape memory alloy from 20 K to 473 K
- 2005
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Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 87:11
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Tidskriftsartikel (refereegranskat)abstract
- The crystal structures, magnetic structures, and phase transformation of the off-stoichiometric Ni53 Mn25 Ga22 were studied by neutron powder diffraction at different temperatures. It is shown that Ni53 Mn25 Ga22 has a tetragonal I4/mmm structure from 20 K to 403 K. An abrupt jump in unit-cell volume around room temperature, corresponding to an endothermic peak in the differential scanning calorimetry curve, was observed. This indicates a pretransformation in the martensitic phase of Ni53 Mn25 Ga22, which is completely different from the phase transformation in the stoichiometric Ni2 MnGa. The sequence of structural transformation in Ni53 Mn25 Ga22 is closely related to its intrinsic temperature-dependent magnetic structure. © 2005 American Institute of Physics.
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| 10. |
- Petrov, Dmitry, et al.
(författare)
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Machine Learning for Large-Scale Quality Control of 3D Shape Models in Neuroimaging
- 2017
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Ingår i: Machine learning in medical imaging. MLMI (Workshop). - Cham : Springer International Publishing. ; 10541, s. 371-378
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Tidskriftsartikel (refereegranskat)abstract
- As very large studies of complex neuroimaging phenotypes become more common, human quality assessment of MRI-derived data remains one of the last major bottlenecks. Few attempts have so far been made to address this issue with machine learning. In this work, we optimize predictive models of quality for meshes representing deep brain structure shapes. We use standard vertex-wise and global shape features computed homologously across 19 cohorts and over 7500 human-rated subjects, training kernelized Support Vector Machine and Gradient Boosted Decision Trees classifiers to detect meshes of failing quality. Our models generalize across datasets and diseases, reducing human workload by 30-70%, or equivalently hundreds of human rater hours for datasets of comparable size, with recall rates approaching inter-rater reliability.
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| 11. |
- Thang, Truong Cong, et al.
(författare)
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Design and implementation of an e-Health system for depression detection
- 2015
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Konferensbidrag (refereegranskat)abstract
- We present the design and implementation of a cost-effective e-Health system for automatic depression detection. The system is based on a client-server architecture, where clients are popular mobile devices. For practical deployment, various factors that affect the accuracy and speed of depression detection are discussed and evaluated with extensive experiments.
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| 12. |
- Wang, Y.D., et al.
(författare)
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Textures and compressive properties of ferromagnetic shape-memory alloy Ni48Mn25Ga22Co5 prepared by isothermal forging process
- 2006
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Ingår i: Journal of Materials Research. - : Springer Science and Business Media LLC. - 0884-2914 .- 2044-5326. ; 21:3, s. 691-697
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Tidskriftsartikel (refereegranskat)abstract
- A ferromagnetic shape-memory alloy Ni48Mn25 Ga22CO5 was prepared by the induction melting and isothermal forging process. Dynamic recrystallization occurs during the isothermal forging. The deformation texture was studied by the neutron diffraction technique. The main texture components consist of (110) [11¯2] and (001) [100], which suggested that in-plane plastic flow anisotropy should be expected in the as-forged condition. The uniaxial compression fracture strain in the forged alloy reaches over 9.5%. The final room-temperature fracture of the polycrystalline Ni48Mn25Ga22CO5 is controlled mainly by intergranular mode.
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| 13. |
- Alshaykh, Mohammed S., et al.
(författare)
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Optical dual-comb Vernier division of an octave-spanning Kerr microcomb
- 2021
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Ingår i: 2021 Conference on Lasers and Electro-Optics, CLEO 2021 - Proceedings.
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Konferensbidrag (refereegranskat)abstract
- We measure the repetition rate of a 900 GHz octave-spanning soliton microcomb based on Vernier dual-comb frequency division implemented with two silicon nitride microresonator combs fabricated on the same wafer.
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| 14. |
- Bao, Chengying, et al.
(författare)
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Observation of Breathing Dark Pulses in Normal Dispersion Optical Microresonators
- 2018
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Ingår i: Physical Review Letters. - 1079-7114 .- 0031-9007. ; 121:25
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Tidskriftsartikel (refereegranskat)abstract
- Breathers are localized waves in nonlinear systems that undergo a periodic variation in time or space. The concept of breathers is useful for describing many nonlinear physical systems including granular lattices, Bose-Einstein condensates, hydrodynamics, plasmas, and optics. In optics, breathers can exist in either the anomalous or the normal dispersion regimes, but they have only been characterized in the former, to our knowledge. Here, externally pumped optical microresonators are used to characterize the breathing dynamics of localized waves in the normal dispersion regime. High-Q optical microresonators featuring normal dispersion can yield mode-locked Kerr combs whose time-domain waveform corresponds to circulating dark pulses in the cavity. We show that with relatively high pump power these Kerr combs can enter a breathing regime, in which the time-domain waveform remains a dark pulse but experiences a periodic modulation on a time scale much slower than the microresonator round trip time. The breathing is observed in the optical frequency domain as a significant difference in the phase and amplitude of the modulation experienced by different spectral lines. In the highly pumped regime, a transition to a chaotic breathing state where the waveform remains dark-pulse-like is also observed, for the first time to our knowledge; such a transition is reversible by reducing the pump power.
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| 15. |
- Baran, Jakub D., et al.
(författare)
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Density Functional Study of Metal-Phthalocyanines Interactions With a Silver Surface Ag(111).
- 2007
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Konferensbidrag (refereegranskat)abstract
- Metal phthalocyanines (MPc) are generally planar organic molecules comprising of a central metal atom surrounded by aromatic rings. Phthalocyanines are structurally similar to important biomolecules such as haemoglobin and chlorophyll and are commonly used in industry for pigmentation. They have been the focus of intense interest due to their electrical and (non-linear) optical properties. Deposited and/or slef-assembled on metal electrodes, phthalocyanines are attractive candidates for novel molecular sensors, memory, and light-harvesting components. Fundamental understanding of molecule-molecule and molecule-surface interaction is important when attempting to determine the charge transport characteristics of metal phthalocyanines. The most important are the interactions between first layer adsorbate molecules and the substrates, since these interactions determine the structural ordering of the organic films and therefore also have a considerable impact on the efficiency of optical, electronic, and magnetic properties of the system. To study the adsorption of metal-phthalocyanines (MPc (M=Co, Sn, Pb) on the Ag(111) surface we have performed electronic structure calculations using a cluster representation of the surface within the framework of density functional theory (DFT) [1]. Our calculations use the generalized gradient approximation (GGA) parameterization by Pedrew-Burke-Ernzerhof (PBE) for the exchange-correlation energy [2]. We have investigated bonding on three surface adsorption sites (hcp-hollow, fcc-hollow and on-top). SnPc was found to adsorb weakly to the surface, and to prefer hollow bonding rather than on-top bonding. The distance between the Sn atom and the top layer Ag-surface atoms (hcp-hollow and fcc-hollow) is consistent with experimental data obtained by normal incidence X-ray standing wave spectroscopy (NIXSW) [3,4]. Adsorption of CoPc was found very site specific and to prefer the on-top binding site. The distance between the Co atom and the top layer Ag atoms is ~3 . For PbPc, successful adsorption was only obtained on the hcp-hollow site. For SnPc and PbPc binding energy is small fraction of eV, however CoPc bind much strongly to Ag(111) .For each of these systems we have found good agreement in binding geometries with experimental data
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| 16. |
- Baran, Jakub D., et al.
(författare)
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DFT Computation Of Metal-Phthalocyanines Bonded To Ag(111)
- 2007
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Konferensbidrag (refereegranskat)abstract
- To study the adsorption of metal-phthalocyanines (MPc (M=Co; Sn; Pb) on the Ag(111) surface we have performed electronic structure calculations using a cluster representation of the surface within the framework of density functional theory (DFT) [1]. Our calculations use the generalized gradient approximation (GGA) parameterization by Pedrew-Burke-Ernzerhof (PBE) for the exchange-correlation energy [2]. We have investigated bonding on three surface adsorption sites (hcp-hollow; fcc-hollow and on-top). SnPc was found to adsorb weakly to the surface (0.15 to 0.25 eV); and to prefer hollow bonding rather than on-top bonding. The distance between the Sn atom and the top layer Ag-surface atoms (hcp-hollow and fcc-hollow) is consistent with experimental data obtained by normal incidence X-ray standing wave spectroscopy (NIXSW) [3;4]. CoPc is much more strongly bound to the Ag(111) surface and was found to prefer the on-top site. The calculated binding energy is 1.2 eV and the distance between the Co atom and the top layer Ag atoms is 3 (which also matched the experimental data well). For PbPc; successful adsorption was only obtained on the hcp-hollow site with a binding energy of 0.5 eV. For each of these systems we have found good agreement in binding geometries with experimental data.
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| 17. |
- Baran, Jakub D., et al.
(författare)
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Interactions of Metal-phthalocyanines MPc (M=Co; Sn; Pb) with Silver Surface Ag(111) : A Density Functional Study
- 2008
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Konferensbidrag (refereegranskat)abstract
- Deposited and/or self-assembled on metal electrodes; metal-phthalocyanine are attractive candidates for novel molecular sensors; memory; and light-harvesting components. The knowledge of the their molecular geometry and electronic structure are crucial points in order to understand their interactions with surfaces. To study the adsorption of metal-phthalocyanines (MPc (M=Co; Sn; Pb) bonded parallel on the Ag(111) surface we have performed electronic structure calculations using a cluster representation (55 and 169 silver atoms) of the surface within the framework of density functional theory (DFT) [1]. Our calculations use the generalized gradient approximation (GGA) parameterization by Pedrew-Burke-Ernzerhof (PBE) for the exchange-correlation energy [2] and multipole accelerated resolution of identity method [3]. We have investigated bonding on three surface adsorption sites (hcp-hollow; fcc-hollow and on-top). For each of these systems we have found good agreement in binding geometries with experimental data obtained by normal incidence X-ray standing wave spectroscopy (NIXSW) [4;5]. Binding energies and geometries for all systems are given. We propose flat chemisorption of respective MPcs on Ag(111).
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| 18. |
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| 19. |
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| 20. |
- Baran, J. D., et al.
(författare)
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Theoretical and experimental comparison of SnPc, PbPc, and CoPc adsorption on Ag(111)
- 2010
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Ingår i: Physical Review B (Condensed Matter and Materials Physics). - 1098-0121 .- 1550-235X. ; 81:7
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Tidskriftsartikel (refereegranskat)abstract
- A combination of normal-incidence x-ray standing-wave (NIXSW) spectroscopy, x-ray photoelectron spectroscopy (XPS), scanning tunneling microscopy (STM), and density-functional theory (DFT) has been used to investigate the interaction of a number of phthalocyanine molecules (specifically, SnPc, PbPc, and CoPc) with the Ag(111) surface. The metal-surface distances predicted by the DFT calculations for SnPc/Ag(111) (2.48 angstrom) and CoPc/Ag(111) (2.88 angstrom) are in good agreement with our NIXSW experimental results for these systems (2.31 +/- 0.09 and 2.90 +/- 0.05 angstrom, respectively). Good agreement is also found between calculated partial density-of-states plots and STM images of CoPc on Ag(111). Although the DFT and Pb 4f NIXSW results for the Pb-Ag(111) distance are similarly in apparently good agreement, the Pb 4f core-level data suggest that a chemical reaction between PbPc and Ag(111) occurs due to the annealing procedure used in our experiments and that the similarity of the DFT and Pb 4f NIXSW values for the Pb-Ag(111) distance is likely to be fortuitous. We interpret the Pb 4f XPS data as indicating that the Pb atom can detach from the PbPc molecule when it is adsorbed in the "Pb-down" position, leading to the formation of a Pb-Ag alloy and the concomitant reduction in Pb from a Pb2+ state (in bulklike films of PbPc) to Pb-0. In contrast to SnPc, neither PbPc nor CoPc forms a well-ordered monolayer on Ag(111) via the deposition and annealing procedures we have used. Our DFT calculations show that each of the phthalocyanine molecules donate charge to the silver surface, and that back donation from Ag to the metal atom (Co, Sn, or Pb) is only significant for CoPc.
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| 21. |
- Beier, Sebastian, et al.
(författare)
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Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.
- 2017
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Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 4
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Tidskriftsartikel (refereegranskat)abstract
- Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. â € Morex' was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).
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| 22. |
- Cong, D Y, et al.
(författare)
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Crystal structures and textures in the hot-forged Ni-Mn-Ga shape memory alloys
- 2006
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Ingår i: Metallurgical and Materials Transactions. A. - 1073-5623 .- 1543-1940. ; 37A:5, s. 1397-1403
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Tidskriftsartikel (refereegranskat)abstract
- Three ferromagnetic shape-memory alloys with the chemical compositions of Ni53Mn25Ga22, Ni48Mn30Ga22, and Ni48Mn25Ga22Co5 were prepared by the induction-melting and hot-forging process. The crystal structures were investigated by the neutron powder diffraction technique, showing that Ni53Mn25Ga22 and Ni48Mn25Ga22Co5 have a tetragonal, I4/mmm martensitic structure at room temperature, while Ni48Mn30Ga22 has a cubic, L2(1) austenitic structure at room temperature. The development of textures in the hot-forged samples shows the in-plane plastic flow anisotropy from the measured pole figures by means of the neutron diffraction technique. Significant texture changes were observed for the Ni48Mn25Ga22Co5 alloy after room temperature deformation, which is due to the deformation-induced rearrangements of martensitic variants. An excellent shape-memory effect (SME) with a recovery ratio of 74 pct was reported in this Ni48Mn25Ga22Co5 polycrystalline alloy after annealing above the martensitic transformation temperature, and the "shape-memory" influence also occurs in the distributions of grain orientations.
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| 23. |
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| 24. |
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| 25. |
- Fan, Tingting, et al.
(författare)
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Bright circularly polarized soft X-ray high harmonics for X-ray magnetic circular dichroism
- 2015
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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. ; 112:46, s. 14206-14211
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Tidskriftsartikel (refereegranskat)abstract
- We demonstrate, to our knowledge, the first bright circularly polarized high-harmonic beams in the soft X-ray region of the electromagnetic spectrum, and use them to implement X-ray magnetic circular dichroism measurements in a tabletop-scale setup. Using counterrotating circularly polarized laser fields at 1.3 and 0.79 mu m, we generate circularly polarized harmonics with photon energies exceeding 160 eV. The harmonic spectra emerge as a sequence of closely spaced pairs of left and right circularly polarized peaks, with energies determined by conservation of energy and spin angular momentum. We explain the single-atom and macroscopic physics by identifying the dominant electron quantum trajectories and optimal phase-matching conditions. The first advanced phase-matched propagation simulations for circularly polarized harmonics reveal the influence of the finite phase-matching temporal window on the spectrum, as well as the unique polarization-shaped attosecond pulse train. Finally, we use, to our knowledge, the first tabletop X-ray magnetic circular dichroism measurements at the N-4,N-5 absorption edges of Gd to validate the high degree of circularity, brightness, and stability of this light source. These results demonstrate the feasibility of manipulating the polarization, spectrum, and temporal shape of high harmonics in the soft X-ray region by manipulating the driving laser waveform.
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| 26. |
- Gutman, Boris A, et al.
(författare)
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A meta-analysis of deep brain structural shape and asymmetry abnormalities in 2,833 individuals with schizophrenia compared with 3,929 healthy volunteers via the ENIGMA Consortium
- 2022
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Ingår i: Human Brain Mapping. - : John Wiley & Sons. - 1065-9471 .- 1097-0193. ; 43:1, s. 352-372
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Tidskriftsartikel (refereegranskat)abstract
- Schizophrenia is associated with widespread alterations in subcortical brain structure. While analytic methods have enabled more detailed morphometric characterization, findings are often equivocal. In this meta-analysis, we employed the harmonized ENIGMA shape analysis protocols to collaboratively investigate subcortical brain structure shape differences between individuals with schizophrenia and healthy control participants. The study analyzed data from 2,833 individuals with schizophrenia and 3,929 healthy control participants contributed by 21 worldwide research groups participating in the ENIGMA Schizophrenia Working Group. Harmonized shape analysis protocols were applied to each site's data independently for bilateral hippocampus, amygdala, caudate, accumbens, putamen, pallidum, and thalamus obtained from T1-weighted structural MRI scans. Mass univariate meta-analyses revealed more-concave-than-convex shape differences in the hippocampus, amygdala, accumbens, and thalamus in individuals with schizophrenia compared with control participants, more-convex-than-concave shape differences in the putamen and pallidum, and both concave and convex shape differences in the caudate. Patterns of exaggerated asymmetry were observed across the hippocampus, amygdala, and thalamus in individuals with schizophrenia compared to control participants, while diminished asymmetry encompassed ventral striatum and ventral and dorsal thalamus. Our analyses also revealed that higher chlorpromazine dose equivalents and increased positive symptom levels were associated with patterns of contiguous convex shape differences across multiple subcortical structures. Findings from our shape meta-analysis suggest that common neurobiological mechanisms may contribute to gray matter reduction across multiple subcortical regions, thus enhancing our understanding of the nature of network disorganization in schizophrenia.
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| 27. |
- Jiang, W., et al.
(författare)
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COVID-19 is associated with bystander polyclonal autoreactive B cell activation as reflected by a broad autoantibody production, but none is linked to disease severity
- 2023
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Ingår i: Journal of Medical Virology. - : Wiley. - 0146-6615 .- 1096-9071. ; 95:1
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Tidskriftsartikel (refereegranskat)abstract
- Coronavirus disease 2019 (COVID-19) is associated with autoimmune features and autoantibody production in a small subset of the population. Pre-existing neutralizing antitype I interferons (IFNs) autoantibodies are related to the severity of COVID-19. Plasma levels of IgG and IgM against 12 viral antigens and 103 self-antigens were evaluated using an antibody protein array in patients with severe/critical or mild/moderate COVID-19 disease and uninfected controls. Patients exhibited increased IgGs against Severe acute respiratory syndrome coronavirus-2 proteins compared to controls, but no difference was observed in the two patient groups. 78% autoreactive IgGs and 93% autoreactive IgMs were increased in patients versus controls. There was no difference in the plasma levels of anti-type I IFN autoantibodies or neutralizing anti-type I IFN activity of plasma samples from the two patient groups. Increased anti-type I IFN IgGs were correlated with higher lymphocyte accounts, suggesting a role of nonpathogenic autoantibodies. Notably, among the 115 antibodies tested, only plasma levels of IgGs against human coronavirus (HCOV)-229E and HCOV-NL63 spike proteins were associated with mild disease outcome. COVID-19 was associated with a bystander polyclonal autoreactive B cell activation, but none of the autoantibody levels were linked to disease severity. Long-term humoral immunity against HCOV-22E and HCOV-NL63 spike protein was associated with mild disease outcome. Understanding the mechanism of life-threatening COVID-19 is critical to reducing mortality and morbidity.
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| 28. |
- Li, L., et al.
(författare)
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Divergence and plasticity shape adaptive potential of the Pacific oyster
- 2018
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Ingår i: Nature Ecology & Evolution. - : Springer Science and Business Media LLC. - 2397-334X. ; 2:11, s. 1751-1760
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Tidskriftsartikel (refereegranskat)abstract
- The interplay between divergence and phenotypic plasticity is critical to our understanding of a species' adaptive potential under rapid climate changes. We investigated divergence and plasticity in natural populations of the Pacific oyster Crassostrea gigas with a congeneric oyster Crassostrea angulata from southern China used as an outgroup. Genome re-sequencing of 371 oysters revealed unexpected genetic divergence in a small area that coincided with phenotypic divergence in growth, physiology, heat tolerance and gene expression across environmental gradients. These findings suggest that selection and local adaptation are pervasive and, together with limited gene flow, influence population structure. Genes showing sequence differentiation between populations also diverged in transcriptional response to heat stress. Plasticity in gene expression is positively correlated with evolved divergence, indicating that plasticity is adaptive and favoured by organisms under dynamic environments. Divergence in heat tolerance-partly through acetylation-mediated energy depression-implies differentiation in adaptive potential. Trade-offs between growth and survival may play an important role in local adaptation of oysters and other marine invertebrates.
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| 29. |
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| 30. |
- Mascher, Martin, et al.
(författare)
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A chromosome conformation capture ordered sequence of the barley genome
- 2017
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 544:7651, s. 427-433
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Tidskriftsartikel (refereegranskat)abstract
- Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.
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| 31. |
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| 32. |
- O'Malley, Nathan P., et al.
(författare)
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RF Stabilization of Vernier Dual-microcombs
- 2023
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Ingår i: 2023 Conference on Lasers and Electro-Optics, CLEO 2023.
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Konferensbidrag (refereegranskat)abstract
- Leveraging the Vernier dual-comb method, we self-reference a THz octave-spanning microcomb with fCEO ~100 GHz - normally too high for typical detection equipment - and translate the stability of an RF reference to optical frequencies.
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| 33. |
- O'Malley, Nathan P., et al.
(författare)
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Vernier Frequency Combs for Stabilization of RF/Optical Links
- 2022
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Ingår i: Optics InfoBase Conference Papers. - 9781957171050
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Konferensbidrag (refereegranskat)abstract
- We utilize the Vernier effect to partially stabilize a pair of high repetition rate, octave-spanning Kerr solitons in silicon nitride microrings fabricated on the same wafer.
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| 34. |
- O'Malley, Nathan P., et al.
(författare)
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Vernier Microcombs for Future Miniature Yb + Clocks
- 2023
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Ingår i: 2023 IEEE Photonics Conference, IPC 2023 - Proceedings.
-
Konferensbidrag (refereegranskat)abstract
- We demonstrate an architecture for dualmicrocomb-based readout of an optical clock. Microcombs frequency-divide a compact narrow-linewidth laser, capable of being frequency-doubled to within a few GHz of a 171Yb+ clock transition, to an RF output.
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| 35. |
- Pham, Tuan D, et al.
(författare)
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Computerized assessment of communication for cognitive stimulation for people with cognitive decline using spectral-distortion measures and phylogenetic inference
- 2015
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Ingår i: PLOS ONE. - San Francisco, CA, United States : Public Library of Science. - 1932-6203. ; 10:3, s. 1-29
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Tidskriftsartikel (refereegranskat)abstract
- Therapeutic communication and interpersonal relationships in care homes can help people to improve their mental wellbeing. Assessment of the efficacy of these dynamic and complex processes are necessary for psychosocial planning and management. This paper presents a pilot application of photoplethysmography in synchronized physiological measurements of communications between the care-giver and people with dementia. Signal-based evaluations of the therapy can be carried out using the measures of spectral distortion and the inference of phylogenetic trees. The proposed computational models can be of assistance and cost-effectiveness in caring for and monitoring people with cognitive decline.
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| 36. |
- Pham, Tuan D, et al.
(författare)
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How Complex Is Cancer Intracellular Signaling Space in FIB-SEM Images?
- 2012
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Ingår i: Sixth UKSim/AMSS European Symposium on Computer Modeling and Simulation (EMS), 2012. - : IEEE Computer Society. - 9781467349772 ; , s. 139-142
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Konferensbidrag (refereegranskat)abstract
- How cell regulates its intracellular features to optimize their signaling pathways is still far from understanding. Recent advancement in microscopy imaging of the structure of cell organelles enables biomedical researchers to study cell morphology in great detail to discover the pathogeneses of diseases by information obtained at molecular level. A particular interest is to quantify the complexity of the spatial content of the intracellular space captured by the combination of focused ion beam (FIB) and scanning electron microscope (SEM) imaging systems. Such quantitative measure of the complexity of organelles is expected to be a useful tool for benchmarking biological simulations of cancers and controlling disease-specific drug effects. In this paper, for the first time nonlinear dynamical models are utilized to investigate the structural characteristics of intracellular space using FIB-SEM technology to quantify the complex architecture of cell organelles.
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| 37. |
- Sahib, Seaab, et al.
(författare)
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Nanodelivery of traditional Chinese Gingko Biloba extract EGb-761 and bilobalide BN-52021 induces superior neuroprotective effects on pathophysiology of heat stroke
- 2021
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Ingår i: Progress in Brain Research. - : Elsevier. - 0079-6123 .- 1875-7855. ; 265, s. 249-315, s. 249-315
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Tidskriftsartikel (refereegranskat)abstract
- Military personnel often exposed to high summer heat are vulnerable to heat stroke (HS) resulting in abnormal brain function and mental anomalies. There are reasons to believe that leakage of the blood-brain barrier (BBB) due to hyperthermia and development of brain edema could result in brain pathology. Thus, exploration of suitable therapeutic strategies is needed to induce neuroprotection in HS. Extracts of Gingko Biloba (EGb-761) is traditionally used in a variety of mental disorders in Chinese traditional medicine since ages. In this chapter, effects of TiO2 nanowired EGb-761 and BN-52021 delivery to treat brain pathologies in HS is discussed based on our own investigations. We observed that TiO2 nanowired delivery of EGb-761 or TiO2 BN-52021 is able to attenuate more that 80% reduction in the brain pathology in HS as compared to conventional drug delivery. The functional outcome after HS is also significantly improved by nanowired delivery of EGb-761 and BN-52021. These observations are the first to suggest that nanowired delivery of EGb-761 and BN-52021 has superior therapeutic effects in HS not reported earlier. The clinical significance in relation to the military medicine is discussed.
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| 38. |
- Setliff, Joshua C., et al.
(författare)
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Single-Stage Correction of Genu Valgum Recurvatum by Distal Femoral and High Tibial Opening Wedge Osteotomies: A Case Report
- 2023
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Ingår i: JBJS case connector. - 2160-3251. ; 13:2
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Tidskriftsartikel (refereegranskat)abstract
- CASE: A 32-year-old woman with genu valgum recurvatum presented to clinic complaining of long-standing anterior knee pain. Radiographs demonstrated a 13° anterior tibial slope and 15° valgus malalignment. She underwent a single-stage 2-level osteotomy at the distal femur and proximal tibia to simultaneously correct genu valgum and recurvatum. This procedure achieved precise correction in both planes. At 1 year, the patient was pain-free and ambulated without restriction. CONCLUSION: This procedure should be considered among the available surgical options when treating genu valgum recurvatum because it produced excellent results for the studied patient.
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| 39. |
- Sharma, Hari Shanker, et al.
(författare)
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Cerebrolysin restores balance between excitatory and inhibitory amino acids in brain following concussive head injury : Superior neuroprotective effects of TiO2 nanowired drug delivery
- 2021
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Ingår i: Brain protection strategies and nanomedicine. - : Elsevier BV. - 9780323989275 ; , s. 211-267
-
Bokkapitel (refereegranskat)abstract
- Concussive head injury (CHI) often associated with military personnel, soccer players and related sports personnel leads to serious clinical situation causing lifetime disabilities. About 3-4 k head injury per 100 k populations are recorded in the United States since 2000-2014. The annual incidence of concussion has now reached to 1.2% of population in recent years. Thus, CHI inflicts a huge financial burden on the society for rehabilitation. Thus, new efforts are needed to explore novel therapeutic strategies to treat CHI cases to enhance quality of life of the victims. CHI is well known to alter endogenous balance of excitatory and inhibitory amino acid neurotransmitters in the central nervous system (CNS) leading to brain pathology. Thus, a possibility exists that restoring the balance of amino acids in the CNS following CHI using therapeutic measures may benefit the victims in improving their quality of life. In this investigation, we used a multimodal drug Cerebrolysin (Ever NeuroPharma, Austria) that is a well-balanced composition of several neurotrophic factors and active peptide fragments in exploring its effects on CHI induced alterations in key excitatory (Glutamate, Aspartate) and inhibitory (GABA, Glycine) amino acids in the CNS in relation brain pathology in dose and time-dependent manner. CHI was produced in anesthetized rats by dropping a weight of 114.6 g over the right exposed parietal skull from a distance of 20 cm height (0.224 N impact) and blood-brain barrier (BBB), brain edema, neuronal injuries and behavioral dysfunctions were measured 8, 24, 48 and 72 h after injury. Cerebrolysin (CBL) was administered (2.5, 5 or 10 mL/kg, i.v.) after 4-72 h following injury. Our observations show that repeated CBL induced a dose-dependent neuroprotection in CHI (5-10 mL/kg) and also improved behavioral functions. Interestingly when CBL is delivered through TiO2 nanowires superior neuroprotective effects were observed in CHI even at a lower doses (2.5-5 mL/kg). These observations are the first to demonstrate that CBL is effectively capable to attenuate CHI induced brain pathology and behavioral disturbances in a dose dependent manner, not reported earlier.
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| 40. |
- Toftegaard, R., et al.
(författare)
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Metal nanoparticle-enhanced radiative transitions: Giving singlet oxygen emission a boost
- 2011
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Ingår i: Pure and Applied Chemistry. - : Walter de Gruyter GmbH. - 1365-3075 .- 0033-4545. ; 83:4, s. 885-898
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Tidskriftsartikel (refereegranskat)abstract
- The fabrication and use of metal nanoparticles to influence electronic transitions in a given molecule is of growing interest; there is much to be gained by developing and exploiting methods to enhance weak optical signals. Singlet molecular oxygen, O-2(a(1)Delta(g)), which is an important intermediate in many oxidation reactions, particularly in biological systems, is ideally monitored by the 1275-nm O-2(a(1)Delta(g)) -> O-2(X-3 Sigma(-)(g)) phosphorescent transition. Unfortunately, the latter is highly forbidden and, as such, often presents a severe limitation in the application of this optical probe. In this paper, we describe how this weak phosphorescent transition can be enhanced by using localized surface plasmons (LSPs) from specially engineered gold nanostructures. In an attempt to elucidate the mechanism of this process, data were recorded from samples in which we decoupled the component of the plasmon resonance that absorbs incident light from the component that scatters incident light. We find that the latter appears to be the feature of significance in the process through which singlet oxygen phosphorescence is enhanced. In this work, we also illustrate how the singlet oxygen system provides an ideal model for a general study of metal-enhanced radiative rate constants.
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| 41. |
- Tran, Minh Cong, et al.
(författare)
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Lung heterogeneity and deadspace volume in acute respiratory distress syndrome animals using the inspired sinewave test
- 2020
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Ingår i: Physiological Measurement. - : IOP Publishing. - 0967-3334 .- 1361-6579. ; 41:11
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Tidskriftsartikel (refereegranskat)abstract
- The acute respiratory distress syndrome is associated with a high rate of morbidity and mortality, as patients undergoing mechanical ventilation are at risk of ventilator-induced lung injuries.OBJECTIVE: To measure the lung heterogeneity and deadspace volume to find safer ventilator strategies. Then, the ventilator settings could offer homogeneous ventilation and theoretically equalise and reduce tidal strain/stress in the lung parenchyma.APPROACH: The Inspired Sinewave Test (IST) is a non-invasive lung measurement tool, which does not require patients' cooperation. The IST can measure the effective lung volume, pulmonary blood flow and deadspace volume. We developed a computational simulation of the cardiopulmonary system to allow lung heterogeneity to be quantified using data solely derived from the IST. Then, the method to quantify lung heterogeneity using two IST tracer gas frequencies (180s and 60s) was introduced and experimented in the simulation lungs and in animal models. Thirteen anaesthetised pigs were studied with the IST, both before and after experimental lung injury (saline-lavage ARDS model). The deadspace volume is compared between IST and the SF_{6} Washout method.RESULTS: The IST could measure the lung heterogeneity using two frequencies tracer gases. Furthermore, the value of IST ventilation heterogeneity in ARDS lungs were higher than in control lungs at PEEP 10cmH_{2}O (AuC=0.85, p<0.001). Deadspace volume values measured by the IST has a strong relationship with the measured values of the SF_{6} (9mL bias and limits of agreement from -79mL to 57mL in control animals).SIGNIFICANCE: the potential impact of the IST technique in the identification of ventilation and perfusion heterogeneity during ventilator support.
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| 42. |
- Wang, Cong, et al.
(författare)
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Inhibition of Wnt/beta-catenin signaling promotes epithelial differentiation of mesenchymal stem cells and repairs bleomycin-induced lung injury
- 2014
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Ingår i: American Journal of Physiology-Cell Physiology. - : American Physiological Society. - 0363-6143 .- 1522-1563. ; 307:3
-
Tidskriftsartikel (refereegranskat)abstract
- Idiopathic pulmonary fibrosis is a progressive lung disorder of unknown etiology. Previous studies have shown that aberrant activation of the Wnt/beta-catenin signaling cascade occurs in lungs of patients with idiopathic pulmonary fibrosis. Given the important roles of the Wnt/beta-catenin signaling pathway in the development of pulmonary fibrosis, we targeted this pathway for the intervention of pulmonary fibrosis with XAV939, a small molecule that specifically inhibits Tankyrase 1/2, eventually leading to the degradation of beta-catenin and suppression of the Wnt/beta-catenin signaling pathway. Our results demonstrated that XAV939 significantly inhibited the activation of Wnt/beta-catenin signaling and attenuated bleomycin-induced lung fibrosis in mice, and thus improved the survival of mice with lung injury. Interestingly, previous investigations have confirmed that endogenous and exogenous mesenchymal stem cells could be recruited to the injured lung, although the exact effects of these cells are debatable. To determine the effect of Wnt/beta-catenin signaling in the epithelial differentiation of bone marrow-derived mesenchymal stem cells (BM-MSCs), we established a coculture system that contains BM-MSCs and alveolar type II epithelial cells. The in vitro experiments demonstrated that XAV939 could promote the differentiation of BM-MSCs into an epithelium-like phenotype in the coculture system. We also found that XAV939 could inhibit the proliferation and myofibroblast differentiation of NIH/3T3 fibroblasts. This work supports that inhibition of the Wnt/beta-catenin signaling pathway may be exploited for the treatment of idiopathic pulmonary fibrosis for which effective treatment strategies are still lacking.
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| 43. |
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| 44. |
- Wang, Jijing, et al.
(författare)
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Testing the link between isoaspartate and Alzheimer's disease etiology
- 2023
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Ingår i: Alzheimer's & Dementia. - : John Wiley & Sons. - 1552-5260 .- 1552-5279. ; 19:4, s. 1491-1502
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Tidskriftsartikel (refereegranskat)abstract
- Isoaspartate (isoAsp) is a damaging amino acid residue formed in proteins as a result of spontaneous deamidation. IsoAsp disrupts protein structures, making them prone to aggregation. Here we strengthened the link between isoAsp and Alzheimer's disease (AD) by novel approaches to isoAsp analysis in human serum albumin (HSA), the most abundant blood protein and a major carrier of amyloid beta (A beta) and phosphorylated tau (p-tau) in blood. We discovered a reduced amount of anti-isoAsp antibodies (P < 0.0001), an elevated isoAsp level in HSA (P < 0.001), more HSA aggregates (P < 0.0001), and increased levels of free A beta (P < 0.01) in AD blood compared to controls. We also found that deamidation significantly reduces HSA capacity to bind with A beta and p-tau (P < 0.05). These suggest the presence in AD of a bottleneck in clearance of A beta and p-tau, leading to their increased concentrations in the brain and facilitating their aggregations there.
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| 45. |
- Wang, Y., et al.
(författare)
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Green Synthesis of Lactone-Based Conjugated Polymers for n-Type Organic Electrochemical Transistors
- 2022
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Ingår i: Advanced Functional Materials. - : Wiley. - 1616-301X .- 1616-3028. ; 32:16
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Tidskriftsartikel (refereegranskat)abstract
- As new and better materials are implemented for organic electrochemical transistors (OECTs), it becomes increasingly important to adopt more economic and environmentally friendly synthesis pathways with respect to conventional transition-metal-catalyzed polymerizations. Herein, a series of novel n-type donor–acceptor-conjugated polymers based on glycolated lactone and bis-isatin units are reported. All the polymers are synthesized via green and metal-free aldol polymerization. The strong electron-deficient lactone-building blocks provide low-lying lowest unoccupied molecular orbital (LUMO) and the rigid backbone needed for efficient electron mobility up to 0.07 cm2 V−1 s−1. Instead, polar atoms in the backbone and ethylene glycol side chains contribute to the ionic conductivity. The resulting OECTs exhibit a normalized maximum transconductance gm,norm of 0.8 S cm−1 and a μC* of 6.7 F cm−1 V−1 s−1. Data on the microstructure show that such device performance originates from a unique porous morphology together with a highly disordered amorphous microstructure, leading to efficient ion-to-electron coupling. Overall, the design strategy provides an inexpensive and metal-free polymerization route for high-performing n-type OECTs.
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| 46. |
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| 47. |
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| 48. |
- Zhang, Huai, et al.
(författare)
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A global survey on the use of the international classification of diseases codes for metabolic dysfunction-associated fatty liver disease.
- 2024
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Ingår i: Hepatology international. - 1936-0541.
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Tidskriftsartikel (refereegranskat)abstract
- With the implementation of the 11th edition of the International Classification of Diseases (ICD-11) and the publication of the metabolic dysfunction-associated fatty liver disease (MAFLD) nomenclature in 2020, it is important to establish consensus for the coding of MAFLD in ICD-11. This will inform subsequent revisions of ICD-11.Using the Qualtrics XM and WJX platforms, questionnaires were sent online to MAFLD-ICD-11 coding collaborators, authors of papers, and relevant association members.A total of 890 international experts in various fields from 61 countries responded to the survey. We also achieved full coverage of provincial-level administrative regions in China. 77.1% of respondents agreed that MAFLD should be represented in ICD-11 by updating NAFLD, with no significant regional differences (77.3% in Asia and 76.6% in non-Asia, p=0.819). Over 80% of respondents agreed or somewhat agreed with the need to assign specific codes for progressive stages of MAFLD (i.e. steatohepatitis) (92.2%), MAFLD combined with comorbidities (84.1%), or MAFLD subtypes (i.e., lean, overweight/obese, and diabetic) (86.1%).This global survey by a collaborative panel of clinical, coding, health management and policy experts, indicates agreement that MAFLD should be coded in ICD-11. The data serves as a foundation for corresponding adjustments in the ICD-11 revision.
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