Palladium-Mediated Formation of Alkyl–Nitrogen Bonds

The following dissertation discusses reactions of palladium complexes to form sp3 carbon–nitrogen bonds. Both stoichiometric reductive elimination reactions to form alkylamines from characterized alkylpalladium(II) complexes and new palladium-catalyzed methods for the synthesis of N-alkylbenzophenone imines are reported.Chapter 1 provides an overview of methods for the N-alkylation of nitrogen nucleophiles. Metal-catalyzed substitution reactions of nitrogen nucleophiles with alkyl electrophiles are discussed with a focus on the fundamental organometallic reactions that may form carbon–nitrogen bonds in these reactions. Examples of reductive elimination reactions from characterized alkylmetal complexes are covered in more detail because of their relevance to later chapters.Chapter 2 discusses continued work in the Hartwig group studying the reductive elimination of norbornylamines from syn-2-methylnorbornylpalladium(II) amido complexes. This work focuses on the effects of phosphine ancillary ligands on the rate of reductive elimination and yield of alkylamine. These studies led to the design of bidentate P,O ligands that stabilize Pd(II) amido complexes while still enabling the reductive elimination of alkylamines to occur in good yield.Chapter 3 presents the reductive elimination of N-neopentyl anilines and N-neopentyl imines from palladium(II) complexes. The P,O ligand structures developed as part of the work described in Chapter 2 proved particularly valuable to the study of neopentylpalladium(II) complexes and enabled the synthesis of stable, four-coordinate Pd(II) anilido and methyleneamido complexes that undergo reductive elimination to form N-neopentyl anilines and N-neopentyl imines in good yields.Chapter 4 discusses the development of palladium catalysts for the cross-coupling of imines and primary alkyl bromides. The addition of fluorinated iminoquinolines as ancillary ligands was found to greatly increase the rate of the reaction. Mechanistic studies suggest that this reaction occurs through a two-electron pathway that may involve oxidative addition to a cyclometallated palladium(II) complex.Chapter 5 expands the palladium-catalyzed cross-coupling of imines to include reactions with synthetically valuable secondary and tertiary alkyl halides. This method was applied to form a variety of imines bearing secondary and tertiary alkyl groups on nitrogen. Mechanistic studies suggest that this reaction occurs through single-electron transfer from a palladium(0) complex to form an alkyl radical intermediate. The intermediacy of this alkyl radical enabled this method to be expanded to include the intramolecular carboamination of unsaturated alkyl bromides

Drug-resistance mechanisms and tuberculosis drugs.

This publication presents independent research supported by the Health Innovation Challenge Fund (HICF-T5-342 and WT098600), a parallel funding partnership between the UK Department of Health and Wellcome Trust.This is the final version of the article. It first appeared at http://dx.doi.org/10.1016/S0140-6736(14)62450-8

Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland.

The correct interpretation of microbial sequencing data applied to surveillance and outbreak investigation depends on accessible genomic databases to provide vital genetic context. Our aim was to construct and describe a United Kingdom MRSA database containing over 1000 methicillin-resistant Staphylococcus aureus (MRSA) genomes drawn from England, Northern Ireland, Wales, Scotland, and the Republic of Ireland over a decade. We sequenced 1013 MRSA submitted to the British Society for Antimicrobial Chemotherapy by 46 laboratories between 2001 and 2010. Each isolate was assigned to a regional healthcare referral network in England and was otherwise grouped based on country of origin. Phylogenetic reconstructions were used to contextualize MRSA outbreak investigations and to detect the spread of resistance. The majority of isolates (n = 783, 77%) belonged to CC22, which contains the dominant United Kingdom epidemic clone (EMRSA-15). There was marked geographic structuring of EMRSA-15, consistent with widespread dissemination prior to the sampling decade followed by local diversification. The addition of MRSA genomes from two outbreaks and one pseudo-outbreak demonstrated the certainty with which outbreaks could be confirmed or refuted. We identified local and regional differences in antibiotic resistance profiles, with examples of local expansion, as well as widespread circulation of mobile genetic elements across the bacterial population. We have generated a resource for the future surveillance and outbreak investigation of MRSA in the United Kingdom and Ireland and have shown the value of this during outbreak investigation and tracking of antimicrobial resistance.We are grateful for assistance from the library construction, sequencing and core informatics teams at the Wellcome Trust Sanger Institute. We acknowledge David Harris and Martin Aslett for their help in submitting the sequenced isolates to public databases. The study was supported by grants from the UKCRC Translational Infection Research Initiative, and the Medical Research Council (Grant Number G1000803) with contributions to the Grant from the Biotechnology and Biological Sciences Research Council, the National Institute for Health Research on behalf of the Department of Health, and the Chief Scientist Office of the Scottish Government Health Directorate (to Prof. Peacock); by Wellcome Trust grant number 098051 awarded to the Wellcome Trust Sanger Institute; and by a Healthcare Infection Society Major Reasearch Grant. MET is a Clinician Scientist Fellow, supported by the Academy of Medical Sciences and the Health Foundation and the NIHR Cambridge Biomedical Research Centre. BGS was supported by Wellcome Trust grant number 089472. The study was approved by the University of Cambridge Human Biology Research Ethics Committee (reference HBREC.2013.05), and by the Cambridge University Hospitals NHS Foundation Trust Research and Development Department (reference A092869). Isolates were supplied by the BSAC Resistance Surveillance Project.This is the final version of the article. It first appeared from Cold Spring Harbor Laboratory Press via http://dx.doi.org/10.1101/gr.196709.11

Preventing kidney transplant failure by screening for antibodies against human leucocyte antigens followed by optimised immunosuppression: OuTSMART RCT

Design: Investigator-led, prospective, open-labelled marker-based strategy (hybrid) randomised trial. Background: Allografts in 3% of kidney transplant patients fail annually. Development of antibodies against human leucocyte antigens is a validated predictive biomarker of allograft failure. Under immunosuppression is recognised to contribute, but whether increasing immunosuppression can prevent allograft failure in human leucocyte antigen Ab+ patients is unclear. Participants: Renal transplant recipients > 1 year post-transplantation attending 13 United Kingdom transplant clinics, without specific exclusion criteria. Interventions: Regular screening for human leucocyte antigen antibodies followed, in positive patients by interview and tailored optimisation of immunosuppression to tacrolimus, mycophenolate mofetil and prednisolone. Objective: To determine if optimisation of immunosuppression in human leucocyte antigen Ab+ patients can cost-effectively prevent kidney allograft failure. Outcome: Time to graft failure after 43 months follow-up in patients receiving the intervention, compared to controls, managed by standard of care. Costs and quality-adjusted life-years were used in the cost-effectiveness analysis. Randomisation and blinding: Random allocation (1 : 1) to unblinded biomarker-led care or double-blinded standard of care stratified by human leucocyte antigen antibodies status (positive/negative) and in positives, presence of donor-specific antibodies (human leucocyte antigen antibodies against donor human leucocyte antigen) or not (human leucocyte antigen antibodies against non-donor human leucocyte antigen), baseline immunosuppression and transplant centre. Biomaker-led care human leucocyte antigen Ab+ patients received intervention. Human leucocyte antigen Ab-negative patients were screened every 8 months. Recruitment Began September 2013 and for 37 months. The primary endpoint, scheduled for June 2020, was moved to March 2020 because of COVID-19. Numbers randomised: From 5519 screened, 2037 were randomised (1028 biomaker-led care, 1009 to standard of care) including 198 with human leucocyte antigen antibodies against donor human leucocyte antigen (106 biomaker-led care, 92 standard of care) and 818 with human leucocyte antigens antibodies against non-donor human leucocyte antigen (427 biomaker-led care, 391 standard of care). Numbers analysed: Two patients were randomised in error so 2035 were included in the intention-to-treat analysis. Outcome: The trial had 80% power to detect a hazard ratio of 0.49 in biomarker-led care DSA+ group, > 90% power to detect hazard ratio of 0.35 in biomarker-led care non-DSA+ group (with 5% type 1 error). Actual hazard ratios for graft failure in these biomarker-led care groups were 1.54 (95% CI: 0.72 to 3.30) and 0.97 (0.54 to 1.74), respectively. There was 90% power to demonstrate non-inferiority of overall biomarker-led care group with assumed hazard ratio of 1.4: This was not demonstrated as the upper confidence limit for graft failure exceeded 1.4: (1.02, 95% CI 0.72 to 1.44). The hazard ratio for biopsy-proven rejection in the overall biomarker-led care group was 0.5 [95% CI: 0.27 to 0.94: p = 0.03]. The screening approach was not cost-effective in terms of cost per quality-adjusted life-year. Harms: No significant differences in other secondary endpoints or adverse events. Limitations: Tailored interventions meant optimisation was not possible in some patients. We did not study pathology on protocol transplant biopsies in DSA+ patients. Conclusions: No evidence that optimised immunosuppression in human leucocyte antigen Ab+ patients delays renal transplant failure. Informing patients of their human leucocyte antigen antibodies status appears to reduce graft rejection. Future work: We need a better understanding of the pathophysiology of transplant failure to allow rational development of effective therapies. Trial registration: This trial is registered as EudraCT (2012-004308-36) and ISRCTN (46157828). Funding: This project was funded by the National Institute for Health and Care Research (NIHR) Efficacy and Mechanism Evaluation programme (11/100/34) and will be published in full in Efficacy and Mechanism Evaluation; Vol. 10, No. 5. See the NIHR Journals Library website for further project information

The WiggleZ Dark Energy Survey: the transition to large-scale cosmic homogeneity

We have made the largest-volume measurement to date of the transition to large-scale homogeneity in the distribution of galaxies. We use the WiggleZ survey, a spectroscopic survey of over 200,000 blue galaxies in a cosmic volume of ~1 (Gpc/h)^3. A new method of defining the 'homogeneity scale' is presented, which is more robust than methods previously used in the literature, and which can be easily compared between different surveys. Due to the large cosmic depth of WiggleZ (up to z=1) we are able to make the first measurement of the transition to homogeneity over a range of cosmic epochs. The mean number of galaxies N(<r) in spheres of comoving radius r is proportional to r^3 within 1%, or equivalently the fractal dimension of the sample is within 1% of D_2=3, at radii larger than 71 \pm 8 Mpc/h at z~0.2, 70 \pm 5 Mpc/h at z~0.4, 81 \pm 5 Mpc/h at z~0.6, and 75 \pm 4 Mpc/h at z~0.8. We demonstrate the robustness of our results against selection function effects, using a LCDM N-body simulation and a suite of inhomogeneous fractal distributions. The results are in excellent agreement with both the LCDM N-body simulation and an analytical LCDM prediction. We can exclude a fractal distribution with fractal dimension below D_2=2.97 on scales from ~80 Mpc/h up to the largest scales probed by our measurement, ~300 Mpc/h, at 99.99% confidence.Comment: 21 pages, 16 figures, accepted for publication in MNRA

The WiggleZ Dark Energy Survey: the growth rate of cosmic structure since redshift z=0.9

We present precise measurements of the growth rate of cosmic structure for the redshift range 0.1 < z < 0.9, using redshift-space distortions in the galaxy power spectrum of the WiggleZ Dark Energy Survey. Our results, which have a precision of around 10% in four independent redshift bins, are well-fit by a flat LCDM cosmological model with matter density parameter Omega_m = 0.27. Our analysis hence indicates that this model provides a self-consistent description of the growth of cosmic structure through large-scale perturbations and the homogeneous cosmic expansion mapped by supernovae and baryon acoustic oscillations. We achieve robust results by systematically comparing our data with several different models of the quasi-linear growth of structure including empirical models, fitting formulae calibrated to N-body simulations, and perturbation theory techniques. We extract the first measurements of the power spectrum of the velocity divergence field, P_vv(k), as a function of redshift (under the assumption that P_gv(k) = -sqrt[P_gg(k) P_vv(k)] where g is the galaxy overdensity field), and demonstrate that the WiggleZ galaxy-mass cross-correlation is consistent with a deterministic (rather than stochastic) scale-independent bias model for WiggleZ galaxies for scales k < 0.3 h/Mpc. Measurements of the cosmic growth rate from the WiggleZ Survey and other current and future observations offer a powerful test of the physical nature of dark energy that is complementary to distance-redshift measures such as supernovae and baryon acoustic oscillations.Comment: 17 pages, 11 figures, accepted for publication by MNRA

BLAST: Correlations in the Cosmic Far-Infrared Background at 250, 350, and 500 microns Reveal Clustering of Star-Forming Galaxies

We detect correlations in the cosmic far-infrared background due to the clustering of star-forming galaxies in observations made with the Balloon-borne Large Aperture Submillimeter Telescope, BLAST, at 250, 350, and 500 microns. We perform jackknife and other tests to confirm the reality of the signal. The measured correlations are well fit by a power law over scales of 5-25 arcminutes, with Delta I/I = 15.1 +/- 1.7%. We adopt a specific model for submillimeter sources in which the contribution to clustering comes from sources in the redshift ranges 1.3 <= z <= 2.2, 1.5 <= z <= 2.7, and 1.7 <= z <= 3.2, at 250, 350, and 500 microns, respectively. With these distributions, our measurement of the power spectrum, P(k_theta), corresponds to linear bias parameters, b = 3.8 +/- 0.6, 3.9 +/- 0.6 and 4.4 +/- 0.7, respectively. We further interpret the results in terms of the halo model, and find that at the smaller scales, the simplest halo model fails to fit our results. One way to improve the fit is to increase the radius at which dark matter halos are artificially truncated in the model, which is equivalent to having some star-forming galaxies at z >= 1 located in the outskirts of groups and clusters. In the context of this model we find a minimum halo mass required to host a galaxy is log (M_min / M_sun) = 11.5 (+0.4/-0.1), and we derive effective biases $b_eff = 2.2 +/- 0.2, 2.4 +/- 0.2, and 2.6 +/- 0.2, and effective masses log (M_eff / M_sun) = 12.9 +/- 0.3, 12.8 +/- 0.2, and 12.7 +/- 0.2, at 250, 350, and 500 microns, corresponding to spatial correlation lengths of r_0 = 4.9, 5.0, and 5.2 +/- 0.7 h^-1 Mpc, respectively. Finally, we discuss implications for clustering measurement strategies with Herschel and Planck.Comment: Accepted for publication in the Astrophysical Journal. Maps and other results available at http://blastexperiment.info