34 results on '"Thomson, Andrew"'
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2. Sublithospheric diamond ages and the supercontinent cycle.
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Timmerman, Suzette, Stachel, Thomas, Koornneef, Janne M., Smit, Karen V., Harlou, Rikke, Nowell, Geoff M., Thomson, Andrew R., Kohn, Simon C., Davies, Joshua H. F. L., Davies, Gareth R., Krebs, Mandy Y., Zhang, Qiwei, Milne, Sarah E. M., Harris, Jeffrey W., Kaminsky, Felix, Zedgenizov, Dmitry, Bulanova, Galina, Smith, Chris B., Cabral Neto, Izaac, and Silveira, Francisco V.
- Abstract
Subduction related to the ancient supercontinent cycle is poorly constrained by mantle samples. Sublithospheric diamond crystallization records the release of melts from subducting oceanic lithosphere at 300–700 km depths1,2 and is especially suited to tracking the timing and effects of deep mantle processes on supercontinents. Here we show that four isotope systems (Rb–Sr, Sm–Nd, U–Pb and Re–Os) applied to Fe-sulfide and CaSiO
3 inclusions within 13 sublithospheric diamonds from Juína (Brazil) and Kankan (Guinea) give broadly overlapping crystallization ages from around 450 to 650 million years ago. The intracratonic location of the diamond deposits on Gondwana and the ages, initial isotopic ratios, and trace element content of the inclusions indicate formation from a peri-Gondwanan subduction system. Preservation of these Neoproterozoic–Palaeozoic sublithospheric diamonds beneath Gondwana until its Cretaceous breakup, coupled with majorite geobarometry3,4, suggests that they accreted to and were retained in the lithospheric keel for more than 300 Myr during supercontinent migration. We propose that this process of lithosphere growth—with diamonds attached to the supercontinent keel by the diapiric uprise of depleted buoyant material and pieces of slab crust—could have enhanced supercontinent stability.The ages and geochemical compositions of inclusions of sublithospheric diamonds indicate additions to the mantle keel of Gondwana by the underplating of buoyant subducted material, originating from 300–700-km depth, which may have contributed to supercontinent stability during long-distance migration. [ABSTRACT FROM AUTHOR]- Published
- 2023
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3. Medical Therapy and Scleral Windows for Uveal Effusion Syndrome: A Case Series and Literature Review.
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Li, Henry H., Hunter, Kaitlyn C., Thomson, Andrew C., and Hunter, Allan A.
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UVEA cancer ,EXUDATES & transudates ,LITERATURE reviews ,RETINAL detachment ,SYNDROMES ,DISEASE progression - Abstract
Introduction: Uveal effusion syndrome (UES) is a rare ocular disease causing idiopathic uveal effusion, often with associated ciliochoroidal and retinal detachment. UES diagnosis is challenging because of overlapping features with other ocular inflammatory, neoplastic, iatrogenic, and drug-induced causes of uveal effusion. While several successful surgical treatments have been described, such as full-thickness or partial-thickness sclerectomy, medical therapies may also have a therapeutic role. Objective: To provide an updated review of the published literature on the course of the disease, medical and surgical management strategies, as well as newer treatment modalities. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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4. Refractive Outcomes After LASIK for the Treatment of Mixed Astigmatism with the Allegretto WaveLight EX500.
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Moshirfar, Majid, Durnford, Kathryn, Megerdichian, Alin, Thomson, Andrew, Martheswaran, Tanisha, West Jr., William, McCabe, Shannon, Ronquillo, Yasmyne, and Hoopes, Philip
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LASIK ,PHOTOREFRACTIVE keratectomy ,ASTIGMATISM ,EXCIMER lasers ,VISUAL acuity ,VECTOR analysis ,LASER industry - Abstract
Introduction: Treatment of mixed astigmatism with laser in situ keratomileusis (LASIK) is complex as the correction requires flattening the cornea in one meridian while steepening the cornea in the other meridian. The bitoric technique has become the most popular approach and has been tested across a variety of platforms. This study is the first to evaluate the results of mixed astigmatism treatment using the Allegretto WaveLight
® EX500. Methods: This study was a single-center, retrospective, noncomparative analysis of 400 eyes that underwent LASIK to correct for mixed astigmatism utilizing the EX500 excimer laser. Data on uncorrected distance visual acuity, corrected distance visual acuity, and spherical equivalent was analyzed at consecutive intervals (1, 3, 6, 9, and 12 months). Refractive measurements were used to perform a vector analysis. Results: Three and 12 months postoperatively, 71% and 74% of eyes had an uncorrected distance visual acuity (UDVA) of 20/20 or better and 99% and 100% of eyes had a UDVA of 20/40 or better, respectively. The postoperative UDVA was within one line of the corrected distance visual acuity (CDVA) in 88% and 93% of eyes at 3 and 12 months, respectively. At 3 months, 78% of eyes achieved refractive astigmatism no greater than 0.50 diopters and at 12 months, 80% achieved this. The mean spherical equivalent refraction was − 0.36 ± 0.57 D at 12 months after surgery. At the 12-month follow-up, the mean refractive cylinder was reduced by 87%, from − 2.79 to − 0.37 diopters. On vector analysis, 99% of eyes had an angle of error within ± 15° from the intended target at 3 and 12 months. Conclusion: Treatment of mixed astigmatism using the Allegretto WaveLight® EX500 laser exceeded the industry standards of safety, efficacy, stability, and accuracy. [ABSTRACT FROM AUTHOR]- Published
- 2022
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5. Prolonged endoscopic retrograde cholangiopancreatography results in higher rates of pancreatitis and unplanned hospitalisation.
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Turbayne, Alexander Keith Bain, Mehta, Abhinav, and Thomson, Andrew
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ENDOSCOPIC retrograde cholangiopancreatography ,INTRAHEPATIC bile ducts ,CHOLANGITIS ,PANCREATIC duct ,PANCREATITIS ,BILE ducts ,GALLSTONES ,HOSPITAL care - Abstract
Background and Aim: Although complications from endoscopic retrograde cholangiopancreatography (ERCP) are well described, procedure duration has received scant attention. The relationship between ERCP duration and patient demographics, indications, results and complications were examined. Methods: A contemporaneously recorded database of 2572 consecutive ERCPs performed between 2008 and 2018 by a single endoscopist was analysed. Those taking under 40 min were compared with those taking over 40 min. Results: Of 2572 cases, 2213 took under 40 min and 359 took over 40 min. Emergency cases (relative risk 2.10), older age (66.6 vs 61.6 years p value < 0.01) and no previous sphincterotomy (relative risk 1.94) were factors which resulted in prolonged procedures. The indication of change or removal of stent for benign conditions resulted in fewer prolonged procedures (relative risk 0.37). Indications of pancreatitis, cholangitis and positive intraoperative cholangiogram were not associated with procedure length. Findings of biliary stricture(s) (relative risk 2.02) and failure to cannulate desired duct (relative risk 3.69) were associated with prolonged procedures. Choledocholithiasis (relative risk 0.62), dilated bile duct without stricture/stone (relative risk 0.46) and normal ductal anatomy (relative risk 0.50) resulted in fewer prolonged procedures. Procedures taking over 40 min had increased risks of complications resulting in unplanned or prolongation of hospitalisation (relative risk 1.41) and pancreatitis (relative risk 1.74). Conclusions: Prolonged procedures had increased rates of pancreatitis and unplanned/prolonged hospitalisation. Failed access to desired duct, advanced age, biliary strictures, no previous sphincterotomy and unplanned emergency cases were associated with prolonged procedures. [ABSTRACT FROM AUTHOR]
- Published
- 2022
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6. PRK Enhancement for Residual Refractive Error After Primary PRK: A Retrospective Study.
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Moshirfar, Majid, Villarreal, Alex, Thomson, Andrew C., West, William B., McCabe, Shannon E., Quinonez Zanabria, Eduardo, Graham, Derrick B., Ronquillo, Yasmyne C., and Hoopes, Phillip C.
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REFRACTIVE errors ,DRUG efficacy ,PHOTOREFRACTIVE keratectomy ,VISUAL acuity ,RETROSPECTIVE studies ,ABERROMETRY - Abstract
Introduction: The efficacy and safety of photorefractive keratectomy (PRK) has been well documented, but outcomes of PRK enhancement following PRK remain understudied. This study aimed to evaluate the safety, efficacy, and predictability of PRK enhancement in patients with residual refractive error after primary PRK and compare these results to prior studies as well as Food and Drug Administration (FDA) safety and efficacy clinical endpoints. Methods: This non-randomized, retrospective chart analysis included eyes with a history of PRK that underwent PRK enhancement at a single center. Post-enhancement data were documented at 3-month and 1-year visits. Patient characteristics between the study group and a control group who underwent primary PRK only were compared. Safety and efficacy measures included change in uncorrected distance visual acuity (UDVA), change in corrected distance visual acuity (CDVA), manifest refraction spherical equivalent (MRSE), amount of induced astigmatism, and presence of serious adverse events. Results: A total of 188 eyes from 141 patients were included. When compared to the control group, women underwent PRK enhancement at a higher rate than men (P = 0.004). The group undergoing PRK enhancement had a higher sphere (P = 0.013) and spherical equivalent (P = 0.004) than the control group at the time of primary PRK. MRSE was reduced to − 0.97 ± 0.72 D (− 2.25 to + 2.13 D) from pre-enhancement values of − 0.98 ± 0.66 D (− 2.75 to + 1.75 D) and stable over 12-month visits with 86% and 98% of eyes within ± 0.50 D and ± 1.00 D of target, respectively. UDVA of 20/20 or better was achieved in 75% of eyes. The UDVA of 75% of eyes remained the same or improved by 1 or more Snellen lines compared with pre-enhancement CDVA. Conclusion: Our results demonstrate that, when compared with previous studies, modern PRK enhancement after PRK has improved visual acuity and refractive outcomes. Though PRK enhancement is not an FDA approved procedure, we show that it meets or exceeds the FDA criteria for the correction of refractive error. [ABSTRACT FROM AUTHOR]
- Published
- 2021
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7. Integration of geoscience frameworks into digital pathology analysis permits quantification of microarchitectural relationships in histological landscapes.
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Kendall, Timothy J., Duff, Catherine M., Thomson, Andrew M., and Iredale, John P.
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GEOLOGY ,HISTOLOGY ,QUANTITATIVE research ,MACHINE learning ,DIAGNOSIS ,PATHOLOGY - Abstract
Although gold-standard histological assessment is subjective it remains central to diagnosis and clinical trial protocols and is crucial for the evaluation of any preclinical disease model. Objectivity and reproducibility are enhanced by quantitative analysis of histological images but current methods require application-specific algorithm training and fail to extract understanding from the histological context of observable features. We reinterpret histopathological images as disease landscapes to describe a generalisable framework defining topographic relationships in tissue using geoscience approaches. The framework requires no user-dependent training to operate on all image datasets in a classifier-agnostic manner but is adaptable and scalable, able to quantify occult abnormalities, derive mechanistic insights, and define a new feature class for machine-learning diagnostic classification. We demonstrate application to inflammatory, fibrotic and neoplastic disease in multiple organs, including the detection and quantification of occult lobular enlargement in the liver secondary to hilar obstruction. We anticipate this approach will provide a robust class of histological data for trial stratification or endpoints, provide quantitative endorsement of experimental models of disease, and could be incorporated within advanced approaches to clinical diagnostic pathology. [ABSTRACT FROM AUTHOR]
- Published
- 2020
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8. Maintaining and breaking symmetry in homomeric coiled-coil assemblies.
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Rhys, Guto G., Wood, Christopher W., Lang, Eric J. M., Mulholland, Adrian J., Brady, R. Leo, Thomson, Andrew R., and Woolfson, Derek N.
- Abstract
In coiled-coil (CC) protein structures α-helices wrap around one another to form rope-like assemblies. Most natural and designed CCs have two–four helices and cyclic (C
n ) or dihedral (Dn ) symmetry. Increasingly, CCs with five or more helices are being reported. A subset of these higher-order CCs is of interest as they have accessible central channels that can be functionalised; they are α-helical barrels. These extended cavities are surprising given the drive to maximise buried hydrophobic surfaces during protein folding and assembly in water. Here, we show that α-helical barrels can be maintained by the strategic placement of β-branched aliphatic residues lining the lumen. Otherwise, the structures collapse or adjust to give more-complex multi-helix assemblies without Cn or Dn symmetry. Nonetheless, the structural hallmark of CCs—namely, knobs-into-holes packing of side chains between helices—is maintained leading to classes of CCs hitherto unobserved in nature or accessed by design. [ABSTRACT FROM AUTHOR]- Published
- 2018
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9. The phase diagrams of KCaF3 and NaMgF3 by ab initio simulations.
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Jakymiw, Clément, Vočadlo, Lidunka, Dobson, David P., Bailey, Edward, Thomson, Andrew R., Brodholt, John P., Wood, Ian G., and Lindsay-Scott, Alex
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SILICATES ,PEROVSKITE ,VOLUMETRIC analysis ,THERMODYNAMICS ,COMPUTER simulation - Abstract
ABF
3 compounds have been found to make valuable low-pressure analogues for high-pressure silicate phases that are present in the Earth’s deep interior and that may also occur in the interiors of exoplanets. The phase diagrams of two of these materials, KCaF3 and NaMgF3 , have been investigated in detail by static ab initio computer simulations based on density functional theory. Six ABF3 polymorphs were considered, as follows: the orthorhombic perovskite structure (GdFeO3 -type; space groupPbnm ); the orthorhombic CaIrO3 structure (Cmcm ; commonly referred to as the “post-perovskite” structure); the orthorhombic Sb2 S3 and La2 S3 structures (bothPmcn ); the hexagonal structure previously suggested in computer simulations of NaMgF3 (P 63 /mmc ); the monoclinic structure found to be intermediate between the perovskite and CaIrO3 structures in CaRhO3 (P 21 /m ). Volumetric and axial equations of state of all phases considered are presented. For KCaF3 , as expected, the perovskite phase is shown to be the most thermodynamically stable at atmospheric pressure. With increasing pressure, the relative stability of the KCaF3 phases then follows the sequence: perovskite → La2 S3 structure → Sb2 S3 structure →P 63 /mmc structure; the CaIrO3 structure is never the most stable form. Above about 2.6 GPa, however, none of the KCaF3 polymorphs are stable with respect to dissociation into KF and CaF2 . The possibility that high-pressure KCaF3 polymorphs might exist metastably at 300 K, or might be stabilised by chemical substitution so as to occur within the standard operating range of a multi-anvil press, is briefly discussed. For NaMgF3 , the transitions to the high-pressure phases occur at pressures outside the normal range of a multi-anvil press. Two different sequences of transitions had previously been suggested from computer simulations. With increasing pressure, we find that the relative stability of the NaMgF3 phases follows the sequence: perovskite → CaIrO3 structure → Sb2 S3 structure →P 63 /mmc structure. However, only the perovskite and CaIrO3 structures are stable with respect to dissociation into NaF and MgF2 . [ABSTRACT FROM AUTHOR]- Published
- 2018
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10. Impact of PV module configuration on energy yield under realistic conditions.
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Thomson, Andrew, Ernst, Marco, Haedrich, Ingrid, and Qian, Jiadong
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PHOTOVOLTAIC cells , *POWER measurement (Electricity) , *THERMAL analysis , *SOLAR radiation , *TETRACHLOROETHYLENE - Abstract
Photovoltaic cell and module manufactures optimise their products according to power measurements performed at a set of standard-test conditions. A key parameter for the financing of a solar project is yield under field or realistic conditions. Field testing modules is time consuming and costly. Hence, we develop a methodology for simulating PV module yield based on the optical, thermal and electrical properties of the components, and the module configuration regarding the cell spacing, interconnection and module layers. With our procedure, we model the performance of standard, half cell and encapsulant free modules in different locations. We present results using our cell to module yield framework for 16 different locations in Australia based on one-minute ground measured solar irradiance and ambient temperature values. We find low-light irradiance losses are directly correlated to the number of cloudy days at a given site. The majority of fielded losses are due to temperature effects, which can be predicted by the average temperature at 3 p.m. We note that wind speed is not accounted for and it will be incorporated in future studies. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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11. Biochemical properties of Paracoccus denitrificans FnrP: reactions with molecular oxygen and nitric oxide.
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Crack, Jason, Hutchings, Matthew, Thomson, Andrew, and Brun, Nick
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PARACOCCUS denitrificans ,NITRIC oxide ,BIOCHEMISTRY ,DENITRIFICATION ,GENETIC regulation ,OXIDATION - Abstract
In Paracoccus denitrificans, three CRP/FNR family regulatory proteins, NarR, NnrR and FnrP, control the switch between aerobic and anaerobic (denitrification) respiration. FnrP is a [4Fe-4S] cluster-containing homologue of the archetypal O sensor FNR from E. coli and accordingly regulates genes encoding aerobic and anaerobic respiratory enzymes in response to O, and also NO, availability. Here we show that FnrP undergoes O-driven [4Fe-4S] to [2Fe-2S] cluster conversion that involves up to 2 O per cluster, with significant oxidation of released cluster sulfide to sulfane observed at higher O concentrations. The rate of the cluster reaction was found to be ~sixfold lower than that of E. coli FNR, suggesting that FnrP can remain transcriptionally active under microaerobic conditions. This is consistent with a role for FnrP in activating expression of the high O affinity cytochrome c oxidase under microaerobic conditions. Cluster conversion resulted in dissociation of the transcriptionally active FnrP dimer into monomers. Therefore, along with E. coli FNR, FnrP belongs to the subset of FNR proteins in which cluster type is correlated with association state. Interestingly, two key charged residues, Arg140 and Asp154, that have been shown to play key roles in the monomer-dimer equilibrium in E. coli FNR are not conserved in FnrP, indicating that different protomer interactions are important for this equilibrium. Finally, the FnrP [4Fe-4S] cluster is shown to undergo reaction with multiple NO molecules, resulting in iron nitrosyl species and dissociation into monomers. [ABSTRACT FROM AUTHOR]
- Published
- 2016
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12. Slab melting as a barrier to deep carbon subduction.
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Thomson, Andrew R., Walter, Michael J., Kohn, Simon C., and Brooker, Richard A.
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- 2016
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13. Monitoring and Evaluating the Effect of Regulatory Action: Some Recent Case Studies.
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Thomson, Andrew, Meeraus, Wilhelmine Hadler, Jenny Wong, and Suvarna, Rafe
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- 2015
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14. A de novo peptide hexamer with a mutable channel.
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Zaccai, Nathan R, Chi, Bertie, Thomson, Andrew R, Boyle, Aimee L, Bartlett, Gail J, Bruning, Marc, Linden, Noah, Sessions, Richard B, Booth, Paula J, Brady, R Leo, and Woolfson, Derek N
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PEPTIDES ,PROTEIN structure ,LEUCINE ,BIOTECHNOLOGY ,ORGANIC compounds - Abstract
The design of new proteins that expand the repertoire of natural protein structures represents a formidable challenge. Success in this area would increase understanding of protein structure and present new scaffolds that could be exploited in biotechnology and synthetic biology. Here we describe the design, characterization and X-ray crystal structure of a new coiled-coil protein. The de novo sequence forms a stand-alone, parallel, six-helix bundle with a channel running through it. Although lined exclusively by hydrophobic leucine and isoleucine side chains, the 6-Å channel is permeable to water. One layer of leucine residues within the channel is mutable, accepting polar aspartic acid and histidine side chains, which leads to subdivision and organization of solvent within the lumen. Moreover, these mutants can be combined to form a stable and unique (Asp-His)
3 heterohexamer. These new structures provide a basis for engineering de novo proteins with new functions. [ABSTRACT FROM AUTHOR]- Published
- 2011
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15. Nitroxide spin labels as EPR reporters of the relaxation and magnetic properties of the heme-copper site in cytochrome bo, E. coli.
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Oganesyan, Vasily, White, Gaye, Field, Sarah, Marritt, Sophie, Gennis, Robert, Yap, Lai, and Thomson, Andrew
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NITROXIDES ,ELECTRON paramagnetic resonance ,SPIN labels ,HEME ,CYTOCHROME b ,ESCHERICHIA coli ,METALLOPROTEINS ,HYDROQUINONE ,SPIN-lattice relaxation - Abstract
nitroxide spin label (SL) has been used to probe the electron spin relaxation times and the magnetic states of the oxygen-binding heme-copper dinuclear site in Escherichia coli cytochrome bo a quinol oxidase (QO), in different oxidation states. The spin lattice relaxation times, T, of the SL are enhanced by the paramagnetic metal sites in QO and hence show a strong dependence on the oxidation state of the latter. A new, general form of equations and a computer simulation program have been developed for the calculation of relaxation enhancement by an arbitrary fast relaxing spin system of S ≥ 1/2. This has allowed us to obtain an accurate estimate of the transverse relaxation time, T, of the dinuclear coupled pair Fe(III)-Cu(II) in the oxidized form of QO that is too short to measure directly. In the case of the F′ state, the relaxation properties of the heme-copper center have been shown to be consistent with a ferryl [Fe(IV)=O] heme and Cu(II) coupled by approximately 1.5-3 cm to a radical. The magnitude suggests that the coupling arises from a radical form of the covalently linked tyrosine-histidine ligand to Cu(II) with unpaired spin density primarily on the tyrosine component. This work demonstrates that nitroxide SLs are potentially valuable tools to probe both the relaxation and the magnetic properties of multinuclear high-spin paramagnetic active sites in proteins that are otherwise not accessible from direct EPR measurements. [ABSTRACT FROM AUTHOR]
- Published
- 2010
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16. The science of RJP Williams.
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Thomson, Andrew
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CHEMICAL elements , *INORGANIC chemistry , *METAL ions , *CALCIUM , *COBALT , *COPPER - Published
- 2016
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17. MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation.
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Tay, Yvonne, Jinqiu Zhang, Thomson, Andrew M., Bing Lim, and Rigoutsos, Isidore
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MESSENGER RNA ,EMBRYONIC stem cells ,GENES ,GENOMES ,RH factor ,EXONS (Genetics) - Abstract
MicroRNAs (miRNAs) are short RNAs that direct messenger RNA degradation or disrupt mRNA translation in a sequence-dependent manner. For more than a decade, attempts to study the interaction of miRNAs with their targets were confined to the 3′ untranslated regions of mRNAs, fuelling an underlying assumption that these regions are the principal recipients of miRNA activity. Here we focus on the mouse Nanog, Oct4 (also known as Pou5f1) and Sox2 genes and demonstrate the existence of many naturally occurring miRNA targets in their amino acid coding sequence (CDS). Some of the mouse targets analysed do not contain the miRNA seed, whereas others span exon–exon junctions or are not conserved in the human and rhesus genomes. miR-134, miR-296 and miR-470, upregulated on retinoic-acid-induced differentiation of mouse embryonic stem cells, target the CDS of each transcription factor in various combinations, leading to transcriptional and morphological changes characteristic of differentiating mouse embryonic stem cells, and resulting in a new phenotype. Silent mutations at the predicted targets abolish miRNA activity, prevent the downregulation of the corresponding genes and delay the induced phenotype. Our findings demonstrate the abundance of CDS-located miRNA targets, some of which can be species-specific, and support an augmented model whereby animal miRNAs exercise their control on mRNAs through targets that can reside beyond the 3′ untranslated region. [ABSTRACT FROM AUTHOR]
- Published
- 2008
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18. Multiphoton-excited luminescence of a lanthanide ion in a protein complex: Tb3+ bound to transferrin.
- Author
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White, Gaye F., Litvinenko, Konstantin L., Meech, Stephen R., Andrews, David L., and Thomson, Andrew J.
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- 2004
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19. mRNA Stability and the Control of Gene Expression: Implications for Human Disease.
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Hollams, Elysia, Giles, Keith, Thomson, Andrew, and Leedman, Peter
- Abstract
Regulation of gene expression is essential for the homeostasis of an organism, playing a pivotal role in cellular proliferation, differentiation, and response to specific stimuli. Multiple studies over the last two decades have demonstrated that the modulation of mRNA stability plays an important role in regulating gene expression. The stability of a given mRNA transcript is determined by the presence of sequences within an mRNA known as cis-elements, which can be bound by trans-acting RNA-binding proteins to inhibit or enhance mRNA decay. These cis-trans interactions are subject to a control by a wide variety of factors including hypoxia, hormones, and cytokines. In this review, we describe mRNA biosynthesis and degradation, and detail the cis-elements and RNA-binding proteins known to affect mRNA turnover. We present recent examples in which dysregulation of mRNA stability has been associated with human diseases including cancer, inflammatory disease, and Alzheimer's disease. [ABSTRACT FROM AUTHOR]
- Published
- 2002
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20. Characterisation of oxidised 7Fe dicluster ferredoxins with NMR spectroscopy.
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Hannan, Jonathan P., Busch, Johanneke L. H., Breton, Jacques, James, Richard, Thomson, Andrew J., Moore, Geoffrey R., and Davy, S. L.
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Dicluster ferredoxins (Fds) from Sulfolobus acidocaldarius and Desulfovibrio africanus (FdIII) have been studied using
1 H NMR. Both wild-type proteins contain a [3Fe-4S]+/0 and a [4Fe-4S]2+/+ cluster as isolated. The [4Fe-4S]2+/+ cluster (cluster II) is bound by cysteine residues arranged in a classic ferredoxin motif: CysI-(Xaa)2 -CysII-(Xaa)2 -CysIII-(Xaa)n -CysIV-Pro, whilst the binding motif of the [3Fe-4S]+/0 cluster (cluster I) has a non-ligating aspartic acid (Asp14) at position II, i.e. CysI-(Xaa)2 -Asp-(Xaa)2 -CysIII. D. africanus FdIII undergoes facile cluster transformation from the 7Fe form to the 8Fe form, but S. acidocaldarius Fd does not. Many factors determine the propensity of a cluster to undergo interconversion, including the presence, and correct orientation, of a suitable ligand. We have investigated this using1 H NMR by introducing a potential fourth ligand into the binding motif of cluster I of D. africanus FdIII. Asp14 has been mutated to cysteine (D14C), glutamic acid (D14E) and histidine (D14H). Cluster incorporation was performed in vitro . The cluster types present were identified from the chemical shift patterns and temperature-dependent behaviour of the hyperfine-shifted resonances. Factors influencing cluster ligation and cluster interconversion, in vitro, are discussed. Furthermore, the data have established that the residue at position II in the cluster binding motif of cluster I is influential in determining the chemical shift pattern observed for a [3Fe-4S]+ cluster when a short/symmetric binding motif is present. Based on this, a series of rules for characterising the1 H NMR chemical shifts of mono- and di-cluster [3Fe-4S]+ cluster-containing ferredoxins is given. [ABSTRACT FROM AUTHOR]- Published
- 2000
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21. Clinicopathologic findings of recurrent primary sclerosing cholangitis after orthotopic liver transplantation.
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Kubota, Toru, Thomson, Andrew, Clouston, Andrew D., Nakazawa, Yuichi, Steadman, Charles, Kerlin, Paul, Shimada, Hiroshi, Balderson, Glenda A., Lynch, Stephen V., and Strong, Russell W.
- Abstract
Whether primary sclerosing cholangitis (PSC) occurs after orthotopic liver transplantation is controversial, largely because the pre-transplant diagnosis of PSC is based on nonspecific radiological and histological findings. We reviewed clinical, radiological, and histological records of 53 patients who underwent liver transplantation for PSC between 1985 and 1998. Three patients with patent hepatic arteries and no evidence of chronic rejection had radiological and histological findings that may have been due to recurrent PSC. Bile duct stricturing in these patients proved permanent and progressive and affected both the quality of life and graft survival. The first patient, who is 110 months after transplantation, has had repeated episodes of cholangitis for the last year. The second patient underwent excision of a strictured hepatic duct 45 months after transplantation and was ultimately retransplanted 95 months after initial transplantation. The third patient underwent left hemihepatectomy of an atrophied lobe 50 months after transplantation. Although the patient population assessed in this study is limited, putative recurrent PSC in the allografts has led either to graft loss or to clinically significant hepatobiliary complications of the graft. [ABSTRACT FROM AUTHOR]
- Published
- 1999
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22. A new Escherichia coli: Bacteroides shuttle vector, pRRI207, based on the Bacteroides ruminicola plasmid replicon pRRI2.
- Author
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Thomson, Andrew, Flint, Harry, Béchet, Max, Martin, Jennifer, and Dubourguier, Henri-Charles
- Abstract
A 3.4kb cryptic plasmid, pRRI2, was isolated from Bacteroides ruminicola 223/M2/7 and used as the basis for a new Bacteroides/Escherichia shuttle vector. Constructs were made incorporating pRRI2, a Bacteroides erythromycin/clindamycin resistance marker and the E. coli pUC8-derived vector pHG165. One of these, pRRI207 (11 kb), was capable of introduction into strains belonging to four different species of Bacteroides (B. uniformis, B. distasonis, B. thetaiotaomicron, or B. ruminicola) either by conjugal transfer from E. coli or by electrotransformation. pRRI207 carries several unique restriction sites derived from the pUC8 multiple cloning site. Only one of six B. ruminicola strains tested was used successfully as a recipient for pRRI207, indicating that further modifications to transfer procedures or marker genes may be needed for wider application in this species. [ABSTRACT FROM AUTHOR]
- Published
- 1992
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23. The Dinuclear Center of Cytochrome bo3 from Escherichia coli.
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Watmough, Nicholas, Cheesman, Myles, Butler, Clive, Little, Richard, Greenwood, Colin, and Thomson, Andrew
- Abstract
For the study of the dinuclear center of heme-copper oxidases cytochrome bo
3 from Escherichia coli offers several advantages over the extensively charactererized bovine cytochrome c oxidase. The availability of strains with enhanced levels of expression allows purification of the significant amounts of enzyme required for detailed spectroscopic studies. Cytochrome bo3 is readily prepared as the fast form, with a homogeneous dinuclear center which gives rise to characteristic broad EPR signals not seen in C cO. The absence of CuA and the incorporation of protohemes allows for a detailed interpretation of the MCD spectra arising from the dinuclear center heme o3 . Careful analysis allows us to distinguish between small molecules that bind to heme o3 , those which are ligands of CuB , and those which react to yield higher oxidation states of heme o3 . Here we review results from our studies of the reactions of fast cytochrome bo3 with formate, fluoride, chloride, azide, cyanide, NO, and H2 O2 . [ABSTRACT FROM AUTHOR]- Published
- 1998
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24. The "prismane" protein resolved: X-ray structure at 1.7 Å and multiple spectroscopy of two novel 4Fe clusters.
- Author
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Arendsen, Alexander F., Hadden, Jonathan, Card, Graeme, McAlpine, Alan S., Bailey, Susan, Zaitsev, Vjacheslav, Duke, Elizabeth H. M., Lindley, P. F., Kröckel, Monika, Trautwein, Alfred X., Feiters, Martinus C., Charnock, John M., Garner, C. David, Marritt, Sophie J., Thomson, Andrew J., Kooter, Ingeborg M., Johnson, Michael K., van den Berg, Willy A. M., van Dongen, Walter M. A. M., and Hagen, W. R.
- Abstract
The three-dimensional structure of the native "putative prismane" protein from Desulfovibrio vulgaris (Hildenborough) has been solved by X-ray crystallography to a resolution of 1.72 Å. The molecule does not contain a [6Fe-6S] prismane cluster, but rather two 4Fe clusters some 12 Å apart and situated close to the interfaces formed by the three domains of the protein. Cluster 1 is a conventional [4Fe-4S] cubane bound, however, near the N-terminus by an unusual, sequential arrangement of four cysteine residues (Cys 3, 6, 15, 21). Cluster 2 is a novel 4Fe structure with two μ
2 -sulfido bridges, two μ2 -oxo bridges, and a partially occupied, unidentified μ2 bridge X. The protein ligands of cluster 2 are widely scattered through the second half of the sequence and include three cysteine residues (Cys 312, 434, 459), one persulfido-cysteine (Cys 406), two glutamates (Glu 268, 494), and one histidine (His 244). With this unusual mixture of bridging and external type of ligands, cluster 2 is named the "hybrid" cluster, and its asymmetric, open structure suggests that it could be the site of a catalytic activity. X-ray absorption spectroscopy at the Fe K-edge is readily interpretable in terms of the crystallographic model when allowance is made for volume contraction at 10 K; no Fe··Fe distances beyond 3.1 Å could be identified. EPR, Mössbauer and MCD spectroscopy have been used to define the oxidation states and the magnetism of the clusters in relation to the crystallographic structure. Reduced cluster 1 is a [4Fe-4S]1+ cubane with S = 3/2; it is the first biological example of a "spin-admixed" iron-sulfur cluster. The hybrid cluster 2 has four oxidation states from (formally) all FeIII to three FeII plus one FeIII . The four iron ions are exchange coupled resulting in the system spins S = 0, 9/2, 0 (and 4), 1/2, respectively, for the four redox states. Resonance Raman spectroscopy suggests that the bridging ligand X which could not be identified unambiguously in the crystal structure is a solvent-exchangeable oxygen. [ABSTRACT FROM AUTHOR]- Published
- 1998
- Full Text
- View/download PDF
25. Microscopic Colitis -- No Longer an Appropriate Term?
- Author
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Thomson, Andrew
- Subjects
TERMS & phrases ,HISTOLOGY ,ETIOLOGY of diseases ,CARCINOGENESIS ,MEDICINE - Abstract
Discusses various aspects of the medical term microscopic colitis. Development of the concept; Histology; Etiology and pathogenesis.
- Published
- 1998
- Full Text
- View/download PDF
26. Hydra Mesoglea Proteome Identifies Thrombospondin as a Conserved Component Active in Head Organizer Restriction.
- Author
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Lommel, Mark, Strompen, Jennifer, Hellewell, Andrew L., Balasubramanian, Gnana Prakash, Christofidou, Elena D., Thomson, Andrew R., Boyle, Aimee L., Woolfson, Derek N., Puglisi, Kane, Hartl, Markus, Holstein, Thomas W., Adams, Josephine C., and Özbek, Suat
- Abstract
Thrombospondins (TSPs) are multidomain glycoproteins with complex matricellular functions in tissue homeostasis and remodeling. We describe a novel role of TSP as a Wnt signaling target in the basal eumetazoan Hydra. Proteome analysis identified Hydra magnipapillata TSP (HmTSP) as a major component of the cnidarian mesoglea. In general, the domain organization of cnidarian TSPs is related to the pentameric TSPs of bilaterians, and in phylogenetic analyses cnidarian TSPs formed a separate clade of high sequence diversity. HmTSP expression in polyps was restricted to the hypostomal tip and tentacle bases that harbor Wnt-regulated organizer tissues. In the hypostome, HmTSP- and Wnt3-expressing cells were identical or in close vicinity to each other, and regions of ectopic tentacle formation induced by pharmacological β-Catenin activation (Alsterpaullone) corresponded to foci of HmTSP expression. Chromatin immunoprecipitation (ChIP) confirmed binding of Hydra TCF to conserved elements in the HmTSP promotor region. Accordingly, β-Catenin knockdown by siRNAs reduced normal HmTSP expression at the head organizer. In contrast, knockdown of HmTSP expression led to increased numbers of ectopic organizers in Alsterpaullone-treated animals, indicating a negative regulatory function. Our data suggest an unexpected role for HmTSP as a feedback inhibitor of Wnt signaling during Hydra body axis patterning and maintenance. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
27. Assessing the relative efficacy of new drugs: an emerging opportunity.
- Author
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Eichler, Hans-Georg, Thomson, Andrew, Eichler, Irmgard, and Schneeweiss, Sebastian
- Subjects
- *
DRUG efficacy , *CLINICAL drug trials , *CLINICAL pharmacology , *RANDOMIZED controlled trials , *PHARMACEUTICAL research - Abstract
The increasing availability of individual-level data from clinical trials could allow the relative efficacy of new drugs to be assessed in a robust, cost-effective and timely way. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
28. Professor Robert JP Williams FRS (25/2/1926-21/3/2015).
- Author
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Thomson, Andrew
- Subjects
- *
METAL ions , *BIOINORGANIC chemistry , *GEOCHEMISTRY , *ENCYCLOPEDIAS & dictionaries , *THERMODYNAMICS - Published
- 2015
- Full Text
- View/download PDF
29. Proteins containing nickel.
- Author
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Thomson, Andrew J.
- Published
- 1982
- Full Text
- View/download PDF
30. The control of chiasma formation in colchicine treated meiocytes of Senecio squalidus.
- Author
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Thomson, Andrew M and Ingram, Ruth
- Published
- 1987
- Full Text
- View/download PDF
31. Earthquake Sounds heard at Great Distances.
- Author
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THOMSON, ANDREW
- Published
- 1929
- Full Text
- View/download PDF
32. Permafrost Drilling and Soil-Temperature Measurements at Resolute, Cornwallis Island, Canada.
- Author
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THOMSON, ANDREW and BREMNER, P. C.
- Published
- 1952
- Full Text
- View/download PDF
33. MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation.
- Author
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Tay, Yvonne, Zhang, Jinqiu, Thomson, Andrew M., Lim, Bing, and Rigoutsos, Isidore
- Subjects
STEM cells - Abstract
An erratum is presented concerning the article "MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation," which was published in the 2008 volume 455 issue.
- Published
- 2009
- Full Text
- View/download PDF
34. Apia Observatory, Samoa.
- Author
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THOMSON, ANDREW and FARR, C. COLERIDGE
- Published
- 1924
- Full Text
- View/download PDF
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