| 1. |
- Kehoe, Laura, et al.
(författare)
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Make EU trade with Brazil sustainable
- 2019
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 364:6438, s. 341-
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 2. |
- Bradnam, K. R., et al.
(författare)
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Assemblathon 2 : Evaluating de novo methods of genome assembly in three vertebrate species
- 2013
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Ingår i: GigaScience. - : BioMed Central (BMC). - 2047-217X. ; 2:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results: In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions: Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.
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| 3. |
- Costeira-Paulo, Joana, et al.
(författare)
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Lipids Shape the Electron Acceptor-Binding Site of the Peripheral Membrane Protein Dihydroorotate Dehydrogenase
- 2018
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Ingår i: Cell Chemical Biology. - : Elsevier BV. - 2451-9456 .- 2451-9448. ; 25:3, s. 309-317
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Tidskriftsartikel (refereegranskat)abstract
- The interactions between proteins and biological membranes are important for drug development, but remain notoriously refractory to structural investigation. We combine non-denaturing mass spectrometry (MS) with molecular dynamics (MD) simulations to unravel the connections among co-factor, lipid, and inhibitor binding in the peripheral membrane protein dihydroorotate dehydrogenase (DHODH), a key anticancer target. Interrogation of intact DHODH complexes by MS reveals that phospholipids bind via their charged head groups at a limited number of sites, while binding of the inhibitor brequinar involves simultaneous association with detergent molecules. MD simulations show that lipids support flexible segments in the membrane-binding domain and position the inhibitor and electron acceptor-binding site away from the membrane surface, similar to the electron acceptor-binding site in respiratory chain complex I. By complementing MS with MD simulations, we demonstrate how a peripheral membrane protein uses lipids to modulate its structure in a similar manner as integral membrane proteins.
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| 4. |
- Drummond, Miguel V., et al.
(författare)
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All-optical generation of 40 Gb/s single sideband signals using a fiber Bragg grating
- 2010
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Ingår i: Optics Communications. - : Elsevier BV. - 0030-4018 .- 1873-0310. ; 283:12, s. 2492-2495
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Tidskriftsartikel (refereegranskat)abstract
- In this work, we demonstrate a reliable all-optical technique for performing optical double sideband (ODSB) to single sideband (OSSB) format conversion of a 40 Gb/s non-return-to-zero signal. It is based on the optimization of a detuned optical filter, which was implemented on a fiber Bragg grating (FBG) with a complex apodization profile. An OSSB signal with negligible distortion was obtained, as the FBG presented a nearly ideal frequency response. Higher tolerance to chromatic dispersion enabled by the OSSB signal in comparison to the ODSB signal was demonstrated on both simulation and experimental results. (C) 2010 Elsevier B.V. All rights reserved.
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| 5. |
- Drummond, Miguel V., et al.
(författare)
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Tunable Optical Dispersion Compensator Based on Power Splitting Between Two Dispersive Media
- 2010
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Ingår i: Journal of Lightwave Technology. - 0733-8724 .- 1558-2213. ; 28:8, s. 1164-1175
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, we propose and experimentally demonstrate a novel tunable optical dispersion compensator (TODC). Dispersion compensation is achieved by splitting the input signal between two dispersive media and adding the resulting signals thereafter. Tunable compensation is attained by controlling the power splitting ratio of the input signal between both dispersive media. The frequency response of the TODC is theoretically assessed considering signal addition in the optical and electrical domains. The latter case is enabled by using optical single side-band (OSSB) modulation, which allows preserving the phase information of dispersive media output signals after direct detection. This is the only case experimentally tested, since it avoids stability problems related with coherent addition of optical signals. A TODC with a tuning range of -340 to 0 ps/nm was designed and experimentally assessed for a 40 Gb/s nonreturn-to-zero OSSB signal. The tunable power splitter consisted of an automatic polarization controller and a polarization beam splitter, which offered a tuning time lower than 150 mu s. A bit error rate lower than 10(-8) was measured on the entire compensation range with a maximum power penalty of 3.3 dB relatively to an SSB signal in back-to-back.
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| 6. |
- Frede, Annika, et al.
(författare)
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B cell expansion hinders the stroma-epithelium regenerative cross talk during mucosal healing
- 2022
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Ingår i: Immunity. - : Elsevier BV. - 1074-7613 .- 1097-4180. ; 55:12, s. 2336-
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Tidskriftsartikel (refereegranskat)abstract
- Therapeutic promotion of intestinal regeneration holds great promise, but defining the cellular mechanisms that influence tissue regeneration remains an unmet challenge. To gain insight into the process of mucosal healing, we longitudinally examined the immune cell composition during intestinal damage and regeneration. B cells were the dominant cell type in the healing colon, and single-cell RNA sequencing (scRNA-seq) re-vealed expansion of an IFN-induced B cell subset during experimental mucosal healing that predominantly located in damaged areas and associated with colitis severity. B cell depletion accelerated recovery upon injury, decreased epithelial ulceration, and enhanced gene expression programs associated with tissue re-modeling. scRNA-seq from the epithelial and stromal compartments combined with spatial transcriptomics and multiplex immunostaining showed that B cells decreased interactions between stromal and epithelial cells during mucosal healing. Activated B cells disrupted the epithelial-stromal cross talk required for orga-noid survival. Thus, B cell expansion during injury impairs epithelial-stromal cell interactions required for mucosal healing, with implications for the treatment of IBD.
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| 7. |
- Loureiro, A., et al.
(författare)
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Size controlled protein nanoemulsions for active targeting of folate receptor positive cells
- 2015
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Ingår i: Colloids and Surfaces B. - : Elsevier. - 0927-7765 .- 1873-4367. ; 135, s. 90-98
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Tidskriftsartikel (refereegranskat)abstract
- Bovine serum albumin (BSA) nanoemulsions were produced by high pressure homogenization with a tri-block copolymer (Poloxamer 407), which presents a central hydrophobic chain of polyoxypropylene (PPO) and two identical lateral hydrophilic chains of polyethylene glycol (PEG). We observed a linear correlation between tri-block copolymer concentration and size - the use of 5. mg/mL of Poloxamer 407 yields nanoemulsions smaller than 100. nm. Molecular dynamics and fluorescent tagging of the tri-block copolymer highlight their mechanistic role on the size of emulsions. This novel method enables the fabrication of highly stable albumin emulsions in the nano-size range, highly desirable for controlled drug delivery. Folic Acid (FA)-tagged protein nanoemulsions were shown to promote specific folate receptor (FR)-mediated targeting in FR positive cells. The novel strategy presented here enables the construction of size controlled, functionalized protein-based nanoemulsions with excellent characteristics for active targeting in cancer therapy.
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| 8. |
- Nogueira, Eugenia, et al.
(författare)
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Peptide Anchor for Folate-Targeted Liposomal Delivery
- 2015
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Ingår i: Biomacromolecules. - : American Chemical Society (ACS). - 1525-7797 .- 1526-4602. ; 16:9, s. 2904-2910
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Tidskriftsartikel (refereegranskat)abstract
- Specific folate receptors are abundantly overexpressed in chronically activated macrophages and in most cancer cells. Directed folate receptor targeting using liposomes is usually achieved using folate linked to a phospholipid or cholesterol anchor. This link is formed using a large spacer like polyethylene glycol. Here, we report an innovative strategy for targeted liposome delivery that uses a hydrophobic fragment of surfactant protein D linked to folate. Our proposed spacer is a small 4 amino acid residue linker. The peptide conjugate inserts deeply into the lipid bilayer without affecting liposomal integrity, with high stability and specificity. To compare the drug delivery potential of both liposomal targeting systems, we encapsulated the nuclear dye Hoechst 34580. The eventual increase in blue fluorescence would only be detectable upon liposome disruption, leading to specific binding of this dye to DNA. Our delivery system was proven to be more efficient (2-fold) in Caco-2 cells than classic systems where the folate moiety is linked to liposomes by polyethylene glycol.
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| 9. |
- Nunes, Silvia C., et al.
(författare)
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Leaf surfaces and neolithization-the case of Arundo donax L
- 2022
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Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- Arundo donax L. (Arundinoideae subfamily, Poaceae family) is a sub-tropical and temperate climate reed that grows in arid and semi-arid environmental conditions, from eastern China to the Mediterranean basin, suggesting potential adaptations at the epicuticular level. A thorough physical-chemical examination of the adaxial and abaxial surfaces of A. donax leaf was performed herein in an attempt to track such chemophenetic adaptations. This sort of approach is of the utmost importance for the current debate about the hypothetical invasiveness of this species in the Mediterranean basin versus its natural colonization along the Plio-Pleistocene period. We concluded that the leaf surfaces contain, apart from stomata, prickles, and long, thin trichomes, and silicon-rich tetralobate phytolits. Chemically, the dominating elements in the leaf ashes are oxygen and potassium; minor amounts of calcium, silicon, magnesium, phosphorous, sulphur, and chlorine were also detected. In both surfaces the epicuticular waxes (whose density is higher in the adaxial surface than in the abaxial surface) form randomly orientated platelets, with irregular shape and variable size, and aggregated rodlets with variable diameter around the stomata. In the case of green mature leaves, the dominating organic compounds of the epicuticular waxes of both surfaces are triterpenoids. Both surfaces feature identical hydrophobic behaviour, and exhibit the same total transmittance, total reflectance, and absorption of incident light. The above findings suggest easy growth of the plant, remarkable epidermic robustness of the leaf, and control of water loss. These chemophenetic characteristics and human influence support a neolithization process of this species along the Mediterranean basin.
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| 10. |
- Penha, Frederico M., et al.
(författare)
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In Situ Observation of Epitaxial Growth during Evaporative Simultaneous Crystallization from Aqueous Electrolytes in Droplets
- 2021
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Ingår i: Crystals. - : MDPI AG. - 2073-4352. ; 11:9, s. 1122-1122
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Tidskriftsartikel (refereegranskat)abstract
- In this study, crystallization phenomena were investigated by real-time in situ observation of seeded droplets under evaporation using a self-developed hot-stage platform. Ternary solutions at eutonic conditions at 25 °C were investigated for the following systems: NaCl–KCl–H2O, NaCl–CaSO4–H2O, and NaCl–Na2SO4–H2O. Evidence of epitaxial growth was found for aqueous NaCl–KCl and aqueous NaCl–Na2SO4. Sodium chloride nucleated and grew epitaxially upon the other substrates in a larger proportion compared with the inverse. This observation could be related to the higher solubility, and consequently higher residual supersaturation of NaCl regarding the other components. Hopper-like NaCl crystals developed in almost all systems. The results may help devise strategies to control particle morphologies and purity in industrial crystallization from complex systems.
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