Baroclinic instability of a meridionally varying basic state

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 1984Several problems are addressed herein. They are loosely connected by the theme of resonant triad interactions. The main topic is the finite amplitude evolution of weakly unstable, linear eigenmodes in a meridionally varying version of Phillips' two-layer model. It is shown in chapter four that interactions between neutral modes and the unstable mode strongly influence the evolution of the latter and are capable of stabilising it before significant changes occur in the zonally averaged flow. The evolution of the unstable wave in the absence of such resonant triad effects is also considered and it is shown by example that the combined influence of changes to the mean flow and higher harmonics of the unstable wave is sufficient to equilibrate the unstable wave. (The higher harmonics are unimportant in the meridionally uniform version of this model). The enhanced importance of neutral sidebands and the details of the evolution are interpreted as being consequences of the structure of the eigenmodes of the linear problem. It is shown in chapter three that, near minimum critical shear, meridional variation of the potential vorticity gradient of the basic flow can introduce dramatic changes in the structure of the normal modes. Some aspects of resonant triad dynamics in a meridionally uniform, vertically sheared, two-layer model are considered in chapter two. It is shown that non-linear interactions between a resonant triplet of neutral waves can lead to baroclinic instability. It is also demonstrated that resonant interactions between a slightly supercritical unstable linear mode and two neutral waves can destabilise the weakly finite amplitude equilibration of the unstable mode that would occur in the absence of the sidebands. This demonstration is limited to the case in which the basic state is not close to minimum critical shear. Finally, the work of Loesch (1974) , who examined the evolution of a weakly unstable mode and a pair of neutral waves in a basic flow that is close to minimum critical shear, is repeated with the difference that critical layer effects are included.The work in this thesis has been supported by the National Science Foundation under grant ATM 79-21-131

The dynamics of an equivalent-barotropic model of the wind-driven circulation

Various steady and time-dependent regimes of a quasi-geostrophic 1.5 layer model of an oceanic circulation driven by a steady wind stress are studied. After being discretized as a numerical model, the quasi-geostrophic equations of motion become a dynamical system with a large dimensional phase space. We find that, for a wide range of parameters, the large-time asymptotic regimes of the model correspond to low-dimensional attractors in this phase space. Motion on these attractors is significant in determining the intrinsic time scales of the system. In two sets of experiments, we explore the dependence of solutions on the viscosity coefficient and the deformation radius. Both experiments yielded a succession of solutions with different forms of time dependence including chaotic solutions. The transition to chaos in this model occurs through a modified classical Ruelle-Takens scenario. We computed some unstable steady regimes of the circulation and the associated fastest growing linear eigenmodes. The structure of the eigenmodes and the details of the energy conversion terms allow us to characterize the primary instability of the steady circulation. It is a complex instability of the western boundary intensification, the western gyre and the meander between the western and central gyres. The model exhibits ranges of parameters in which multiple, stable, time-dependent solutions exist. Further, we note that some bifurcations involve the appearance of variability at climatological time scales, purely as a result of the intrinsic dynamics of the wind-driven circulation

1991 Summer Study Program in Geophysical Fluid Dynamics : patterns in fluid flow

The GFD program in 1991 focused on pattern forming processes in physics and geophysics. The pricipallecturer, Stephan Fauve, discussed a variety of systems, including our old favorite, Rayleigh-Bénard convection, but passing on to exotic examples such as vertically vibrated granular layers. Fauve's lectures emphasize a unified theoretical viewpoint based on symmetry arguments. Patterns produced by instabilties can be described by amplitude equations, whose form can be deduced by symmetry arguments, rather than the asymptotic expansions that have been the staple of past Summer GFD Programs. The amplitude equations are far simpler than the complete equations of motion, and symetry arguments are easier than asymptotic expansions. Symmetry arguments also explain why diverse systems are often described by the same amplitude equation. Even for granular layers, where there is not a universaly accepted continuum description, the appropnate amplitude equation can often be found using symmetry arguments and then compared with experiment. Our second speaker, Daniel Rothan, surveyed the state of the art in lattice gas computations. His lectures illustrate the great utility of these methods in simulating the flow of complex multiphase fluids, particularly at low Reynolds numbers. The lattice gas simulations reveal a complicated phenomenology much of which awaits analytic exploration. The fellowship lectures cover broad ground and reflect the interests of the staff members associated with the program. They range from the formation of sand dunes, though the theory of lattice gases, and on to two dimensional-turbulence and convection on planetary scales. Readers desiring to quote from these report should seek the permission of the authors (a partial list of electronic mail addresses is included on page v). As in previous years, these reports are extensively reworked for publication or appear as chapters in doctoral theses. The task of assembling the volume in 1991 was at first faciltated by our newly acquired computers, only to be complicated by hurricane Bob which severed electric power to Walsh Cottage in the final hectic days of the Summer.Funding was provided by the National Science Foundation through Grant No. OCE 8901012

The programme on ecosystem change and society (PECS)–a decade of deepening social-ecological research through a place-based focus

The Programme on Ecosystem Change and Society (PECS) was established in 2011, and is now one of the major international social-ecological systems (SES) research networks. During this time, SES research has undergone a phase of rapid growth and has grown into an influential branch of sustainability science. In this Perspective, we argue that SES research has also deepened over the past decade, and helped to shed light on key dimensions of SES dynamics (e.g. system feedbacks, aspects of system design, goals and paradigms) that can lead to tangible action for solving the major sustainability challenges of our time. We suggest four ways in which the growth of place-based SES research, fostered by networks such as PECS, has contributed to these developments, namely by: 1) shedding light on transformational change, 2) revealing the social dynamics shaping SES, 3) bringing together diverse types of knowledge, and 4) encouraging reflexive researchers

Halochromic coordination polymers based on a triarylmethane dye for reversible detection of acids

Chromeazurol B (Na2HL) is a pH-sensitive (halochromic) dye based on a hydroxytriarylmethane core and two carboxylate functional groups, which makes it suitable for the synthesis of coordination polymers. Two new coordination polymers [NaZn4(H2O)3(L)3]·3THF·3H2O (1) and [Zn3(H2O)3(μ2- OH2)(μ3-OH)(HL)2(H2L)]·2THF·3H2O (2) incorporating Chromeazurol B linkers have been prepared and characterised. The structure of 1 comprises pentanuclear heterometallic {Zn4Na} nodes linked by six L3– anions to give a layered structure with a honeycomb topology. 2 crystallizes as a double-chain ribbon (ladder) structure with two types of metal node: a mononuclear Zn(II) cation and tetranuclear {Zn(II)}4 cluster. Chromeazurol B anions link each tetranuclear cluster to four individual Zn(II) cations and each Zn(II) cation with four tetranuclear clusters. Both compounds show pH-sensitivity in water solution which can be observed visually, giving the first example of a halochromic coordination polymer. The halochromic properties of 1 towards HCl vapors were systematically investigated. As-synthesized violet-grey 1 reversibly changes color from orange to pink in the presence of vapors of 2M and 7M HCl, respectively. The coordination of the Chromeazurol B anion at each color stage was examined by diffuse reflectance spectroscopy and FT-IR measurements. The remarkable stability of 1 to acid and the observed reversible and reproducible color changes provide a new design for multifunctional sensor materials

Transcriptional diversity during lineage commitment of human blood progenitors.

Blood cells derive from hematopoietic stem cells through stepwise fating events. To characterize gene expression programs driving lineage choice, we sequenced RNA from eight primary human hematopoietic progenitor populations representing the major myeloid commitment stages and the main lymphoid stage. We identified extensive cell type-specific expression changes: 6711 genes and 10,724 transcripts, enriched in non-protein-coding elements at early stages of differentiation. In addition, we found 7881 novel splice junctions and 2301 differentially used alternative splicing events, enriched in genes involved in regulatory processes. We demonstrated experimentally cell-specific isoform usage, identifying nuclear factor I/B (NFIB) as a regulator of megakaryocyte maturation-the platelet precursor. Our data highlight the complexity of fating events in closely related progenitor populations, the understanding of which is essential for the advancement of transplantation and regenerative medicine.The work described in this article was primarily supported by the European Commission Seventh Framework Program through the BLUEPRINT grant with code HEALTH-F5-2011-282510 (D.H., F.B., G.C., J.H.A.M., K.D., L.C., M.F., S.C., S.F., and S.P.G.). Research in the Ouwehand laboratory is further supported by program grants from the National Institute for Health Research (NIHR, www.nihr.ac.uk; to A.A., M.K., P.P., S.B.G.J., S.N., and W.H.O.) and the British Heart Foundation under nos. RP-PG-0310-1002 and RG/09/12/28096 (www.bhf.org.uk; to A.R. and W.J.A.). K.F. and M.K. were supported by Marie Curie funding from the NETSIM FP7 program funded by the European Commission. The laboratory receives funding from the NHS Blood and Transplant for facilities. The Cambridge BioResource (www.cambridgebioresource.org.uk), the Cell Phenotyping Hub, and the Cambridge Translational GenOmics laboratory (www.catgo.org.uk) are supported by an NIHR grant to the Cambridge NIHR Biomedical Research Centre (BRC). The BRIDGE-Bleeding and Platelet Disorders Consortium is supported by the NIHR BioResource—Rare Diseases (http://bioresource.nihr.ac.uk/; to E.T., N.F., and Whole Exome Sequencing effort). Research in the Soranzo laboratory (L.V., N.S., and S. Watt) is further supported by the Wellcome Trust (Grant Codes WT098051 and WT091310) and the EU FP7 EPIGENESYS initiative (Grant Code 257082). Research in the Cvejic laboratory (A. Cvejic and C.L.) is funded by the Cancer Research UK under grant no. C45041/A14953. S.J.S. is funded by NIHR. M.E.F. is supported by a British Heart Foundation Clinical Research Training Fellowship, no. FS/12/27/29405. E.B.-M. is supported by a Wellcome Trust grant, no. 084183/Z/07/Z. Research in the Laffan laboratory is supported by Imperial College BRC. F.A.C., C.L., and S. Westbury are supported by Medical Research Council Clinical Training Fellowships, and T.B. by a British Society of Haematology/NHS Blood and Transplant grant. R.J.R. is a Principal Research Fellow of the Wellcome Trust, grant no. 082961/Z/07/Z. Research in the Flicek laboratory is also supported by the Wellcome Trust (grant no. 095908) and EMBL. Research in the Bertone laboratory is supported by EMBL. K.F. and C.v.G. are supported by FWO-Vlaanderen through grant G.0B17.13N. P.F. is a compensated member of the Omicia Inc. Scientific Advisory Board. This study made use of data generated by the UK10K Consortium, derived from samples from the Cohorts arm of the project.This is the author’s version of the work. It is posted here by permission of the AAAS for personal use, not for redistribution. The definitive version was published in Science on 26/9/14 in volume 345, number 6204, DOI: 10.1126/science.1251033. This version will be under embargo until the 26th of March 2015

The programme on ecosystem change and society (PECS) – a decade of deepening social-ecological research through a place-based focus

The Programme on Ecosystem Change and Society (PECS) was established in 2011, and is now one of the major international social-ecological systems (SES) research networks. During this time, SES research has undergone a phase of rapid growth and has grown into an influential branch of sustainability science. In this Perspective, we argue that SES research has also deepened over the past decade, and helped to shed light on key dimensions of SES dynamics (e.g. system feedbacks, aspects of system design, goals and paradigms) that can lead to tangible action for solving the major sustainability challenges of our time. We suggest four ways in which the growth of place-based SES research, fostered by networks such as PECS, has contributed to these developments, namely by: 1) shedding light on transformational change, 2) revealing the social dynamics shaping SES, 3) bringing together diverse types of knowledge, and 4) encouraging reflexive researchers

The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease

Many common variants have been associated with hematological traits, but identification of causal genes and pathways has proven challenging. We performed a genome-wide association analysis in the UK Biobank and INTERVAL studies, testing 29.5 million genetic variants for association with 36 red cell, white cell, and platelet properties in 173,480 European-ancestry participants. This effort yielded hundreds of low frequency (<5%) and rare (<1%) variants with a strong impact on blood cell phenotypes. Our data highlight general properties of the allelic architecture of complex traits, including the proportion of the heritable component of each blood trait explained by the polygenic signal across different genome regulatory domains. Finally, through Mendelian randomization, we provide evidence of shared genetic pathways linking blood cell indices with complex pathologies, including autoimmune diseases, schizophrenia, and coronary heart disease and evidence suggesting previously reported population associations between blood cell indices and cardiovascular disease may be non-causal.We thank members of the Cambridge BioResource Scientific Advisory Board and Management Committee for their support of our study and the National Institute for Health Research Cambridge Biomedical Research Centre for funding. K.D. is funded as a HSST trainee by NHS Health Education England. M.F. is funded from the BLUEPRINT Grant Code HEALTH-F5-2011-282510 and the BHF Cambridge Centre of Excellence [RE/13/6/30180]. J.R.S. is funded by a MRC CASE Industrial studentship, co-funded by Pfizer. J.D. is a British Heart Foundation Professor, European Research Council Senior Investigator, and National Institute for Health Research (NIHR) Senior Investigator. S.M., S.T, M.H, K.M. and L.D. are supported by the NIHR BioResource-Rare Diseases, which is funded by NIHR. Research in the Ouwehand laboratory is supported by program grants from the NIHR to W.H.O., the European Commission (HEALTH-F2-2012-279233), the British Heart Foundation (BHF) to W.J.A. and D.R. under numbers RP-PG-0310-1002 and RG/09/12/28096 and Bristol Myers-Squibb; the laboratory also receives funding from NHSBT. W.H.O is a NIHR Senior Investigator. The INTERVAL academic coordinating centre receives core support from the UK Medical Research Council (G0800270), the BHF (SP/09/002), the NIHR and Cambridge Biomedical Research Centre, as well as grants from the European Research Council (268834), the European Commission Framework Programme 7 (HEALTH-F2-2012-279233), Merck and Pfizer. DJR and DA were supported by the NIHR Programme ‘Erythropoiesis in Health and Disease’ (Ref. NIHR-RP-PG-0310-1004). N.S. is supported by the Wellcome Trust (Grant Codes WT098051 and WT091310), the EU FP7 (EPIGENESYS Grant Code 257082 and BLUEPRINT Grant Code HEALTH-F5-2011-282510). The INTERVAL study is funded by NHSBT and has been supported by the NIHR-BTRU in Donor Health and Genomics at the University of Cambridge in partnership with NHSBT. The views expressed are those of the authors and not necessarily those of the NHS, the NIHR, the Department of Health of England or NHSBT. D.G. is supported by a “la Caixa”-Severo Ochoa pre-doctoral fellowship

Phenotypic Characterization of EIF2AK4 Mutation Carriers in a Large Cohort of Patients Diagnosed Clinically With Pulmonary Arterial Hypertension.

BACKGROUND: Pulmonary arterial hypertension (PAH) is a rare disease with an emerging genetic basis. Heterozygous mutations in the gene encoding the bone morphogenetic protein receptor type 2 (BMPR2) are the commonest genetic cause of PAH, whereas biallelic mutations in the eukaryotic translation initiation factor 2 alpha kinase 4 gene (EIF2AK4) are described in pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis. Here, we determine the frequency of these mutations and define the genotype-phenotype characteristics in a large cohort of patients diagnosed clinically with PAH. METHODS: Whole-genome sequencing was performed on DNA from patients with idiopathic and heritable PAH and with pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis recruited to the National Institute of Health Research BioResource-Rare Diseases study. Heterozygous variants in BMPR2 and biallelic EIF2AK4 variants with a minor allele frequency of <1:10 000 in control data sets and predicted to be deleterious (by combined annotation-dependent depletion, PolyPhen-2, and sorting intolerant from tolerant predictions) were identified as potentially causal. Phenotype data from the time of diagnosis were also captured. RESULTS: Eight hundred sixty-four patients with idiopathic or heritable PAH and 16 with pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis were recruited. Mutations in BMPR2 were identified in 130 patients (14.8%). Biallelic mutations in EIF2AK4 were identified in 5 patients with a clinical diagnosis of pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis. Furthermore, 9 patients with a clinical diagnosis of PAH carried biallelic EIF2AK4 mutations. These patients had a reduced transfer coefficient for carbon monoxide (Kco; 33% [interquartile range, 30%-35%] predicted) and younger age at diagnosis (29 years; interquartile range, 23-38 years) and more interlobular septal thickening and mediastinal lymphadenopathy on computed tomography of the chest compared with patients with PAH without EIF2AK4 mutations. However, radiological assessment alone could not accurately identify biallelic EIF2AK4 mutation carriers. Patients with PAH with biallelic EIF2AK4 mutations had a shorter survival. CONCLUSIONS: Biallelic EIF2AK4 mutations are found in patients classified clinically as having idiopathic and heritable PAH. These patients cannot be identified reliably by computed tomography, but a low Kco and a young age at diagnosis suggests the underlying molecular diagnosis. Genetic testing can identify these misclassified patients, allowing appropriate management and early referral for lung transplantation