An organic geochemical approach to problems of glacial-interglacial climatic variability

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 May 1988The concentration and carbon isotopic composition (δ13C) of sedimentary organic carbon (Corg), N/C ratios, and terrigenous and marine δ13C-Corg end-members form a basis from which to address problems of Late Quaternary glacial-interglacial climatic variability in a 208.7 m hydraulic piston core (DSDP 619) from the Pigmy Basin in the northern Gulf of Mexico. Paired analyses of δ13C-Corg and N/C are consistent with the hypothesis that the sedimentary organic carbon in the Pigmy Basin is a climatically-determined mixture of C3-photosynthetic terrigenous and marine organic matter, confirming the model of Sackett (1964). A high resolution (~1.4-2.7 ky/sample) δ13C-Corg record shows that sedimentary organic carbon in interglacial oxygen isotope (sub)stages 1 and 5a-b are enriched in 13C (average ± 10 values are -24.2 ± 1.2% 0 and -23.0 ± 0.8% relative to PDB, respectively) while glacial isotope stage values 2 are relatively depleted (-25.6 ± 0.5%). Concentrations of terrigenous and marine sedimentary organic carbon are calculated using δ13C-Corg and Corg measurements, and terrigenous and marine δ13C-Corg end-members. The net accumulation rate of terrigenous organic carbon is 3.7±3.1 times higher in isotope stages 2-4 than in (sub)stages 1 and 5a-b, recording higher erosion rates of terrigenous organic material in glacial periods than interglacial periods. The concentration and net accumulation rates of marine and terrigenous Corg suggest that the nutrient-bearing plume of the Mississippi River may have advanced and retreated across the Pigmy Basin as sea level fell and rose in response to glacial-interglacial sea level change. A study of selected organic biomarker compounds which could serve as tracers of terrigenous and marine sedimentary organic matter sources was performed by comparison with contemporaneous sedimentary organic carbon isotopic composition (δ13C-Corg). Organic carbon-normalized concentrations of total long chain (C37-C39) unsaturated alkenones and individual C27-C29 desmethyl sterols were determined to be useful proportional indicators of preserved marine and terrigenous organic carbon, respectively. The a1kenones, whose source is marine phytoplankton of the class Prymnesiophyceae, generally occurred in higher concentrations in interglacial isotope stages 1 and 5a-b than in the intervening stages, including glacial stages 2 and 4. Sterols (C27-C29) of a dominantly terrigenous origin had lower concentrations during interglacial stages than in glacial stages. The sedimentary records of both terrigenous and marine organic carbon-normalized biomarker compound concentrations appear to be systematically altered by the remineralization of sedimentary organic carbon, as indicated by a simple, first-order organic carbon decay model. The sedimentary deposition of some terrigenous 4-desmethy1stero1s may be affected by differential hydraulic particle sorting as they are transported from river deltas across the continental shelf and slope to the hemipelagic Pigmy Basin. The marine phytoplanktonic alkenones which originate in the surface ocean and sink through the water column would not be subject to comparable particle sorting. The lack of any 4-desmethyl- or 4-α-methy1sterol which was linearly related to the proportion of marine sedimentary organic matter (as scaled by δ13C-Corg) indicated that either (1) sedimentary diagenesis had obscured the biomarker/Corg versus δ13C-Corg record, or (2) the selected compounds were not proportional indicators of preserved marine organic carbon input. The diagenetic alteration of the sedimentary sterol concentration records in which marine sterols were apparently more susceptible to degradation than terrigenous sterols was consistent with present-day sediment trap and recent (10-1-102y) sediment core observations. Preferential preservation of terrigenous sterols may result in a biased sedimentary record of sterol input which could be misinterpreted as indicating solely terrigenous sterol sources. The value and limitations of a simple model which characterizes the effects of sedimentary diagenesis and source input changes on the relationship between organic carbon-normalized biomarker compounds and sedimentary organic matter carbon isotopic composition are discussed. The potential occurrence of sterol double bond hydrogenations (Δ5',Δ22) in three classes of C27-29-4-desmethy1stero1s was evaluated by examining the time series of expected product/precursor relationships with sterol data from the ~2-100kybp DSDP 619 record. Only the Δ5-hydrogenations of the C29 sterols (24-ethy1cholest-5-en- 3β-01, 24-ethylcholesta-5,22-dien-3β-01) showed significant temporally-increasing trends. The 24-ethy1cho1estan-3β-01/24-ethy1cho1est- 5-en-3β-ol (C29Δ°/C29Δ5) ratio also positively correlated with paired sedimentary organic carbon isotopic composition (δ13C-Corg) values. This may be due to increased susceptibility to diagenetic transformation reactions by the organic matter accompanying finer grain-sized terrigenous sediment particles. A long-term source change of 24-ethylcholestan-3β-01 relative to 24-ethylcholest-5-en-3β-01 to explain the correlation with δ13C-Corg seems less likely since both compounds are predominantly of a terrigenous origin in the Pigmy Basin. A comparison of histograms of stanol/stenol (ΔO/Δ5) ratios for the C27-29 -4-desmethylsterols indicates the following sequence in the relative degree of tranformation: C27 > C28 > C29. The C27 - and C28-sterols appear to have attained their respective degrees of transformation before -2kybp, perhaps prior to deposition in the Pigmy Basin. However, differential rates of competing reactions of both the precursor and products may have obscured these simple transformation ratio records. The sedimentary record of a ratio (Uk37) of long chain (C37) unsaturated alkenones is a useful indicator of glacial-interglacial climatic change in the Late Quaternary northern Gulf of Mexico where a planktonic foraminiferal δ18O-CaCO3 record is complicated by meltwater and/or fluvial events (Williams and Kohl, 1986). Using laboratory temperature calibration data of the Uk37 ratio (Prahl and Wakeham, 1987), it is suggested that the minimum glacial surface mixed layer (SML) temperature was 8±1°C colder than the Holocene high SML temperature of 25.6±O.5°C in a Pigmy Basin hydraulic piston core (DSDP 619). However, this glacial-interglacial Uk37-temperature difference was significantly larger than the differences predicted by either the foraminiferal δ18O or foraminiferal assemblage temperature methods (O.8-2.0°C). A possible cause for this large difference is that the Prymnesiophyte assemblages in this area may vary in response to climatically-induced hydrographic changes. Interglacial periods may be dominated by pelagic Prymnesiophyte assemblages, while glacial periods may be dominated by neritic assemblages. Correlation of the Uk37 ratio with the sedimentary organic carbon composition (δ13C-Corg) is consistent with the predominance of preserved input of erosive terrigenous over marine organic carbon during glacial stages in the northern Gulf of Mexico when sea level was as much as 150m lower than in the present interglacial stage. Marine organic carbon burial dominated in warmer interglacial stages 1 and 5a-b

Revealing charge-tunneling processes between a quantum dot and a superconducting island through gate sensing

We report direct detection of charge-tunneling between a quantum dot and a superconducting island through radio-frequency gate sensing. We are able to resolve spin-dependent quasiparticle tunneling as well as two-particle tunneling involving Cooper pairs. The quantum dot can act as an RF-only sensor to characterize the superconductor addition spectrum, enabling us to access subgap states without transport. Our results provide guidance for future dispersive parity measurements of Majorana modes, which can be realized by detecting the parity-dependent tunneling between dots and islands.Comment: 6 pages, 4 figures, supplemental material included as ancillary fil

FAIR data retrieval for sensitive clinical research data in Galaxy

Background: In clinical research, data have to be accessible and reproducible, but the generated data are becoming larger and analysis complex. Here we propose a platform for Findable, Accessible, Interoperable, and Reusable (FAIR) data access and creating reproducible findings. Standardized access to a major genomic repository, the European Genome-Phenome Archive (EGA), has been achieved with API services like PyEGA3. We aim to provide a FAIR data analysis service in Galaxy by retrieving genomic data from the EGA and provide a generalized “omics” platform for FAIR data analysis. Results: To demonstrate this, we implemented an end-to-end Galaxy workflow to replicate the findings from an RD-Connect synthetic dataset Beyond the 1 Million Genomes (synB1MG) available from the EGA. We developed the PyEGA3 connector within Galaxy to easily download multiple datasets from the EGA. We added the gene.iobio tool, a diagnostic environment for precision genomics, to Galaxy and demonstrate that it provides a more dynamic and interpretable view for trio analysis results. We developed a Galaxy trio analysis workflow to determine the pathogenic variants from the synB1MG trios using the GEMINI and gene.iobio tool. The complete workflow is available at WorkflowHub, and an associated tutorial was created in the Galaxy Training Network, which helps researchers unfamiliar with Galaxy to run the workflow. Conclusions: We showed the feasibility of reusing data from the EGA in Galaxy via PyEGA3 and validated the workflow by rediscovering spiked-in variants in synthetic data. Finally, we improved existing tools in Galaxy and created a workflow for trio analysis to demonstrate the value of FAIR genomics analysis in Galaxy.</p

The chiral phase transition in charge ordered 1T-TiSe2

It was recently discovered that the low temperature, charge ordered phase of 1T-TiSe2 has a chiral character. This unexpected chirality in a system described by a scalar order parameter could be explained in a model where the emergence of relative phase shifts between three charge density wave components breaks the inversion symmetry of the lattice. Here, we present experimental evidence for the sequence of phase transitions predicted by that theory, going from disorder to non-chiral and finally to chiral charge order. Employing X-ray diffraction, specific heat, and electrical transport measurements, we find that a novel phase transition occurs ~7 K below the main charge ordering transition in TiSe2, in agreement with the predicted hierarchy of charge ordered phases.Comment: 5 pages, 3 figures; includes additional experimental and theoretical results; fixed typo

Rapid Detection of Coherent Tunneling in an InAs Nanowire Quantum Dot through Dispersive Gate Sensing

Dispersive sensing is a powerful technique that enables scalable and high-fidelity readout of solid-state quantum bits. In particular, gate-based dispersive sensing has been proposed as the readout mechanism for future topological qubits, which can be measured by single electrons tunneling through zero-energy modes. The development of such a readout requires resolving the coherent charge tunneling amplitude from a quantum dot in a Majorana-zero-mode host system faithfully on short time scales. Here, we demonstrate rapid single-shot detection of a coherent single-electron tunneling amplitude between InAs nanowire quantum dots. We have realized a sensitive dispersive detection circuit by connecting a sub-GHz, lumped element microwave resonator to a high-lever arm gate on one of dots. The resulting large dot-resonator coupling leads to an observed dispersive shift that is of the order of the resonator linewidth at charge degeneracy. This shift enables us to differentiate between Coulomb blockade and resonance, corresponding to the scenarios expected for qubit state readout, with a signal to noise ratio exceeding 2 for an integration time of 1 microsecond. Our result paves the way for single shot measurements of fermion parity on microsecond timescales in topological qubits.Comment: 6 pages, 4 figure

Efficacy of pulmonary artery pressure monitoring in patients with chronic heart failure:a meta-analysis of three randomized controlled trials

Aims Adjustment of treatment based on remote monitoring of pulmonary artery (PA) pressure may reduce the risk of hospital admission for heart failure (HF). We have conducted a meta-analysis of large randomized trials investigating this question. Methods A systematic literature search was performed for randomized clinical trials with PA pressure monitoring devices in patients and results with HF. The primary outcome of interest was the total number of HF hospitalizations. Other outcomes assessed were urgent visits leading to treatment with intravenous diuretics, all-cause mortality, and composites. Treatment effects are expressed as hazard ratios, and pooled effect estimates were obtained applying random effects meta-analyses. Three eligible randomized clinical trials were identified that included 1898 outpatients in New York Heart Association functional classes II–IV, either hospitalized for HF in the prior 12 months or with elevated plasma NT-proBNP concentrations. The mean followup was 14.7 months, 67.8% of the patients were men, and 65.8% had an ejection fraction ≤40%. Compared to patients in the control group, the hazard ratio (95% confidence interval) for total HF hospitalizations in those randomized to PA pressure monitoring was 0.70 (0.58–0.86) (P = .0005). The corresponding hazard ratio for the composite of total HF hospitalizations, urgent visits and all-cause mortality was 0.75 (0.61–0.91; P = .0037) and for all-cause mortality 0.92 (0.73–1.16). Subgroup analyses, including ejection fraction phenotype, revealed no evidence of heterogeneity in the treatment effect. Conclusion The use of remote PA pressure monitoring to guide treatment of patients with HF reduces episodes of worsening HF and subsequent hospitalizations.</p

Synthesis of trace element bearing single crystals of Chlor-Apatite (Ca5(PO4)3Cl) using the flux growth method

We present a new strategy on how to synthesize trace-element bearing (REE, Sr) chlorapatites Ca5(PO4)3Cl using the flux growth method. Synthetic apatites were up to several mm long, light blue in colour. The apatites were characterized using XRD, electron microprobe and laser ablation ICP-MS (LA-ICPMS) techniques and contained several hundred μg/g La, Ce, Pr, Sm, Gd and Lu and about 1700 μg/g Sr. The analyses indicate that apatites were homogenous (within the uncertainties) for major and trace elements

A network analysis to identify pathophysiological pathways distinguishing ischaemic from non-ischaemic heart failure

Aims Heart failure (HF) is frequently caused by an ischaemic event (e.g. myocardial infarction) but might also be caused by a primary disease of the myocardium (cardiomyopathy). In order to identify targeted therapies specific for either ischaemic or non‐ischaemic HF, it is important to better understand differences in underlying molecular mechanisms. Methods and results We performed a biological physical protein–protein interaction network analysis to identify pathophysiological pathways distinguishing ischaemic from non‐ischaemic HF. First, differentially expressed plasma protein biomarkers were identified in 1160 patients enrolled in the BIOSTAT‐CHF study, 715 of whom had ischaemic HF and 445 had non‐ischaemic HF. Second, we constructed an enriched physical protein–protein interaction network, followed by a pathway over‐representation analysis. Finally, we identified key network proteins. Data were validated in an independent HF cohort comprised of 765 ischaemic and 100 non‐ischaemic HF patients. We found 21/92 proteins to be up‐regulated and 2/92 down‐regulated in ischaemic relative to non‐ischaemic HF patients. An enriched network of 18 proteins that were specific for ischaemic heart disease yielded six pathways, which are related to inflammation, endothelial dysfunction superoxide production, coagulation, and atherosclerosis. We identified five key network proteins: acid phosphatase 5, epidermal growth factor receptor, insulin‐like growth factor binding protein‐1, plasminogen activator urokinase receptor, and secreted phosphoprotein 1. Similar results were observed in the independent validation cohort. Conclusions Pathophysiological pathways distinguishing patients with ischaemic HF from those with non‐ischaemic HF were related to inflammation, endothelial dysfunction superoxide production, coagulation, and atherosclerosis. The five key pathway proteins identified are potential treatment targets specifically for patients with ischaemic HF

Photosynthetic fractionation of ¹³C and concentrations of dissolved CO₂ in the central equatorial Pacific during the last 255,000 years

Carbon isotopically based estimates of CO₂ levels have been generated from a record of the photosynthetic fractionation of ¹³C (≡εp) in a central equatorial Pacific sediment core that spans the last ~255 ka. Contents of ¹³C in phytoplanktonic biomass were determined by analysis of C37 alkadienones. These compounds are exclusive products of Prymnesiophyte algae which at present grow most abundantly at depths of 70-90 m in the central equatorial Pacific. A record of the isotopic composition of dissolved CO₂ was constructed from isotopic analyses of the planktonic foraminifera Neogloboquadrina dutertrei, which calcified at 70-90 m in the same region. Values of εp, derived by comparison of the organic and inorganic δ values, were transformed to yield concentrations of dissolved CO₂ (≡ce) based on a new, site-specific calibration of the relationship between εp and ce. The calibration was based on reassessment of existing εp versus ce data, which support a physiologically based model in which εp is inversely related to ce. Values of P CO₂, the partial pressure of CO₂ that would be in equilibrium with the estimated concentrations of dissolved CO₂, were calculated using Henry’s law and the temperature determined from the alkenone-unsaturation index UK′37. Uncertainties in these values arise mainly from uncertainties about the appropriateness (particularly over time) of the site-specific relationship between εp and 1/ce. These are discussed in detail and it is concluded that the observed record of εp most probably reflects significant variations in ∆p CO₂, the ocean-atmosphere disequilibrium, which appears to have ranged from ~110 μatm during interglacials. Fluxes of CO₂ to the atmosphere would thus have been significantly larger during glacial intervals. If this were characteristic of large areas of the equatorial Pacific, then greater glacial sinks for the equatorially evaded CO₂ must have existed elsewhere. Statistical analysis of air-sea p CO₂ differences and other parameters revealed significant (p<0.01) inverse correlations of ∆p CO₂, with sea surface temperature and with the mass accumulation rate of opal. The former suggests response to the strength of upwelling, the latter may indicate either drawdown of CO₂ by siliceous phytoplankton or variation of [CO₂]/[Si(OH)₄] ratios in upwelling waters

Observation of 2e-periodic Supercurrents in Nanowire Single-Cooper-Pair Transistors

Parity control of superconducting islands hosting Majorana zero modes (MZMs) is required to operate topological qubits made from proximitized semiconductor nanowires. We, therefore, study parity effects in hybrid InAs-Al single-Cooper-pair transistors (SCPTs) as a first step. In particular, we investigate the gate-charge supercurrent modulation and observe a consistent 2$e$-periodic pattern indicating a general lack of low-energy subgap states in these nanowires at zero magnetic field. In a parallel magnetic field, an even-odd pattern develops with a gate-charge spacing that oscillates as a function of field demonstrating that the modulation pattern is sensitive to the presence of a single subgap state. In addition, we find that the parity lifetime of the SCPT decreases exponentially with magnetic field as the subgap state approaches zero energy. Our work highlights the important role that intentional quasiparticle traps and superconducting gap engineering would play in topological qubits that require quenching of the island charge dispersion.Comment: 8 pages, 4 figures, supplemental material included as ancillary fil