Linking education and hospital data in England: linkage process and quality

Introduction: Linkage of administrative data for universal state education and National Health Service (NHS) hospital care would enable research into the inter-relationships between education and health for all children in England. / Objectives: We aim to describe the linkage process and evaluate the uality of linkage of four one-year birth cohorts within the National Pupil Database (NPD) and Hospital Episode Statistics (HES). / Methods: We used multi-step deterministic linkage algorithms to link longitudinal records from state schools to the chronology of records in the NHS Personal Demographics Service (PDS; linkage stage 1), and HES (linkage stage 2). We calculated linkage rates and compared pupil characteristics in linked and unlinked samples for each stage of linkage and each cohort (1990/91, 1996/97, 1999/00, and 2004/05). / Results: Of the 2,287,671 pupil records, 2,174,601 (95%) linked to HES. Linkage rates improved over time (92% in 1990/91 to 99% in 2004/05). Ethnic minority pupils and those living in more deprived areas were less likely to be matched to hospital records, but differences in pupil characteristics between linked and unlinked samples were moderate to small. Conclusion We linked nearly all pupils to at least one hospital record. The high coverage of the linkage represents a unique opportunity for wide-scale analyses across the domains of health and education. However, missed links disproportionately affected ethnic minorities or those living in the poorest neighbourhoods: selection bias could be mitigated by increasing the quality and completeness of identifiers recorded in administrative data or the application of statistical methods that account for missed links

The structure of the deubiquitinase USP15 reveals a misaligned catalytic triad and an open ubiquitin-binding channel

© 2018 Ward et al. Ubiquitin-specific protease 15 (USP15) regulates important cellular processes, including transforming growth factor β (TGF-β) signaling, mitophagy, mRNA processing, and innate immune responses; however, structural information on USP15's catalytic domain is currently unavailable. Here, we determined crystal structures of the USP15 catalytic core domain, revealing a canonical USP fold, including a finger, palm, and thumb region. Unlike for the structure of paralog USP4, the catalytic triad is in an inactive configuration with the catalytic cysteine ∼10 Å apart from the catalytic histidine. This conformation is atypical, and a similar misaligned catalytic triad has so far been observed only for USP7, although USP15 and USP7 are differently regulated. Moreover, we found that the active-site loops are flexible, resulting in a largely open ubiquitin tail-binding channel. Comparison of the USP15 and USP4 structures points to a possible activation mechanism. Sequence differences between these two USPs mainly map to the S1' region likely to confer specificity, whereas the S1 ubiquitin-binding pocket is highly conserved. Isothermal titration calorimetry monoubiquitin- and linear diubiquitin-binding experiments showed significant differences in their thermodynamic profiles, with USP15 displaying a lower affinity for monoubiquitin than USP4. Moreover, we report that USP15 is weakly inhibited by the antineoplastic agent mitoxantrone in vitro A USP15-mitoxantrone complex structure disclosed that the anthracenedione interacts with the S1' binding site. Our results reveal first insights into USP15's catalytic domain structure, conformational changes, differences between paralogs, and small-molecule interactions and establish a framework for cellular probe and inhibitor development

Discovery of peptide ligands targeting a specific ubiquitin-like domain– binding site in the deubiquitinase USP11

© 2019 Spiliotopoulos et al. Published by The American Society for Biochemistry and Molecular Biology, Inc. Ubiquitin-specific proteases (USPs) reverse ubiquitination and regulate virtually all cellular processes. Defined noncatalytic domains in USP4 and USP15 are known to interact with E3 ligases and substrate recruitment factors. No such interactions have been reported for these domains in the paralog USP11, a key regulator of DNA double-strand break repair by homologous recombination. We hypothesized that USP11 domains adjacent to its protease domain harbor unique peptide-binding sites. Here, using a next-generation phage display (NGPD) strategy, combining phage display library screening with next-generation sequencing, we discovered unique USP11-interacting peptide motifs. Isothermal titration calorimetry disclosed that the highest affinity peptides (K D of 10 M) exhibit exclusive selectivity for USP11 over USP4 and USP15 in vitro. Furthermore, a crystal structure of a USP11–peptide complex revealed a previously unknown binding site in USP11’s noncatalytic ubiquitin-like (UBL) region. This site interacted with a helical motif and is absent in USP4 and USP15. Reporter assays using USP11-WT versus a binding pocket– deficient double mutant disclosed that this binding site modulates USP11’s function in homologous recombination–mediated DNA repair. The highest affinity USP11 peptide binder fused to a cellular delivery sequence induced significant nuclear localization and cell cycle arrest in S phase, affecting the viability of different mammalian cell lines. The USP11 peptide ligands and the paralog-specific functional site in USP11 identified here provide a framework for the development of new biochemical tools and therapeutic agents. We propose that an NGPD-based strategy for identifying interacting peptides may be applied also to other cellular targets

Universal DNA methylation age across mammalian tissues

Aging, often considered a result of random cellular damage, can be accurately estimated using DNA methylation profiles, the foundation of pan-tissue epigenetic clocks. Here, we demonstrate the development of universal pan-mammalian clocks, using 11,754 methylation arrays from our Mammalian Methylation Consortium, which encompass 59 tissue types across 185 mammalian species. These predictive models estimate mammalian tissue age with high accuracy (r > 0.96). Age deviations correlate with human mortality risk, mouse somatotropic axis mutations and caloric restriction. We identified specific cytosines with methylation levels that change with age across numerous species. These sites, highly enriched in polycomb repressive complex 2-binding locations, are near genes implicated in mammalian development, cancer, obesity and longevity. Our findings offer new evidence suggesting that aging is evolutionarily conserved and intertwined with developmental processes across all mammals

Quantifying uncertainties from mobile-laboratory-derived emissions of well pads using inverse Gaussian methods

Mobile laboratory measurements provide information on the distribution of CH4 emissions from point sources such as oil and gas wells, but uncertainties are poorly constrained or justified. Sources of uncertainty and bias in ground-based Gaussian-derived emissions estimates from a mobile platform were analyzed in a combined field and modeling study. In a field campaign where 1009 natural gas sites in Pennsylvania were sampled, a hierarchical measurement strategy was implemented with increasing complexity. Of these sites,  ∼ 93&thinsp;% were sampled with an average of 2 transects in  &lt; 5&thinsp;min (standard sampling),  ∼ 5&thinsp;% were sampled with an average of 10 transects in  &lt; 15&thinsp;min (replicate sampling) and  ∼ 2&thinsp;% were sampled with an average of 20 transects in 15–60&thinsp;min. For sites sampled with 20 transects, a tower was simultaneously deployed to measure high-frequency meteorological data (intensive sampling). Five of the intensive sampling sites were modeled using large eddy simulation (LES) to reproduce CH4 concentrations in a turbulent environment. The LES output and LES-derived emission estimates were used to compare with the results of a standard Gaussian approach. The LES and Gaussian-derived emission rates agreed within a factor of 2 in all except one case; the average difference was 25&thinsp;%. A controlled release was also used to investigate sources of bias in either technique. The Gaussian method agreed with the release rate more closely than the LES, underlining the importance of inputs as sources of uncertainty for the LES. The LES was also used as a virtual experiment to determine an optimum number of repeat transects and spacing needed to produce representative statistics. Approximately 10 repeat transects spaced at least 1&thinsp;min apart are required to produce statistics similar to the observed variability over the entire LES simulation period of 30&thinsp;min. Sources of uncertainty from source location, wind speed, background concentration and atmospheric stability were also analyzed. The largest contribution to the total uncertainty was from atmospheric variability; this is caused by insufficient averaging of turbulent variables in the atmosphere (also known as random errors). Atmospheric variability was quantified by repeat measurements at individual sites under relatively constant conditions. Accurate quantification of atmospheric variability provides a reasonable estimate of the lower bound for emission uncertainty. The uncertainty bounds calculated for this work for sites with  &gt; 50&thinsp;ppb enhancements were 0.05–6.5q (where q is the emission rate) for single-transect sites and 0.5–2.7q for sites with 10+ transects. More transects allow a mean emission rate to be calculated with better precision. It is recommended that future mobile monitoring schemes quantify atmospheric variability, and attempt to minimize it, under representative conditions to accurately estimate emission uncertainty. These recommendations are general to mobile-laboratory-derived emissions from other sources that can be treated as point sources.</p

Syntheses and Electronic Properties of Rhodium(III) Complexes Bearing a Redox-Active Ligand

A series of rhodium(III) complexes of the redox-active ligand, H(L = bis(4-methyl-2-(1H-pyrazol-1-yl)phenyl)amido), was prepared, and the electronic properties were studied. Thus, heating an ethanol solution of commercial RhCl3·3H2O with H(L) results in the precipitation of insoluble [H(L)]RhCl3, 1. The reaction of a methanol suspension of [H(L)]RhCl3 with NEt4OH causes ligand deprotonation and affords nearly quantitative yields of the soluble, deep-green, title compound (NEt4)[(L)RhCl3]·H2O, 2·H2O. Complex 2·H2O reacts readily with excess pyridine, triethylphosphine, or pyrazine (pyz) to eliminate NEt4Cl and give charge-neutral complexes trans-(L)RhCl2(py), trans-3, trans-(L)RhCl2(PEt3), trans- 4, or trans-(L)RhCl2(pyz), trans-5, where the incoming Lewis base is trans- to the amido nitrogen of the meridionally coordinating ligand. Heating solutions of complexes trans-3 or trans-4 above about 100 °C causes isomerization to the appropriate cis-3 or cis-4. Isomerization of trans-5 occurs at a much lower temperature due to pyrazine dissociation. Cis-3 and cis- 5 could be reconverted to their respective trans- isomers in solution at 35 °C by visible light irradiation. Complexes [(L)Rh(py)2Cl](PF6), 6, [(L)Rh(PPh3)(py)Cl](PF6), 7, [(L)Rh(PEt3)2Cl](PF6), 8, and [(L)RhCl(bipy)](OTf = triflate), 9, were prepared from 2·H2O by using thallium(I) salts as halide abstraction agents and excess Lewis base. It was not possible to prepare dicationic complexes with three unidentate pyridyl or triethylphosphine ligands; however, the reaction between 2, thallium(I) triflate, and the tridentate 4′-(4-methylphenyl)-2,2′:6′,2″-terpyridine (ttpy) afforded a high yield of [(L)Rh(ttpy)]- (OTf)2, 10. The solid state structures of nine new complexes were obtained. The electrochemistry of the various derivatives in CH2Cl2 showed a ligand-based oxidation wave whose potential depended mainly on the charge of the complex, and to a lesser extent on the nature and the geometry of the other supporting ligands. Thus, the oxidation wave for 2 with an anionic complex was found at +0.27 V versus Ag/AgCl in CH2Cl2, while those waves for the charge-neutral complexes 3−5 were found between +0.38 to +0.59 V, where the cis- isomers were about 100 mV more stable toward oxidation than the trans- isomers. The oxidation waves for 6−9 with monocationic complexes occurred in the range +0.74 to 0.81 V while that for 10 with a dicationic complex occurred at +0.91 V. Chemical oxidation of trans-3, cis-3, and 8 afforded crystals of the singly oxidized complexes, [trans- (L)RhCl2(py)](SbCl6), cis-[(L)RhCl2(py)](SbCl4)·2CH2Cl2, and [(L)Rh(PEt3)2Cl](SbCl6)2, respectively. Comparisons of structural and spectroscopic features combined with the results of density functional theory (DFT) calculations between nonoxidized and oxidized forms of the complexes are indicative of the ligand-centered radicals in the oxidized derivatives

Counteranion-Dependent Reaction Pathways in the Protonation of Cationic Ruthenium−Vinylidene Complexes

The tetraphenylborate salts of the cationic vinylidene complexes [Cp*Ru=C=CHR(iPr2PNHPy)]+ (R = p-C6H4CF3 (1a-BPh4), Ph (1b-BPh4), p-C6H4CH3 (1c- BPh4), p-C6H4Br (1d-BPh4), tBu (1e-BPh4), H (1f-BPh4)) have been protonated using an excess of HBF4·OEt2 in CD2Cl2, furnishing the dicationic carbyne complexes [Cp*Ru≡CCH2R(iPr2PNHPy)]2+ (R = p-C6H4CF3 (2a), Ph (2b), p-C6H4CH3 (2c), p-C6H4Br (2d), tBu (2e), H (2f)), which were characterized in solution at low temperature by NMR spectroscopy. The corresponding reaction of the chloride salts 1a-Cl, 1b-Cl, 1c-Cl, and 1d-Cl followed a different pathway, instead affording the novel alkene complexes [Cp*RuCl(κ1(N),η2(C,C)-C5H4N-NHPiPr2CH=CHR)][BF4] (3a−d). In these species, the entering proton is located at the α- carbon atom of the former vinylidene ligand, which also forms a P−C bond with the phosphorus atom of the iPr2PNHPy ligand. To shed light on the reaction mechanism, DFT calculations have been performed by considering several protonation sites. The computational results suggest metal protonation followed by insertion. The coordination of chloride to ruthenium leads to alkenyl species which can undergo a P−C coupling to yield the corresponding alkene complexes. The noncoordinating nature of [BPh4]− does not allow the stabilization of the unsaturated species coming from the insertion step, thus preventing this alternative pathway