Description: 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 September 1991

Description: In this thesis, I study the time-varying behavior of a ventila ted thermocline with basin scales at annual and decadal time scales. The variability is forced by three external forcings: the wind stress (chapter 3), the surface heat flux (chapter 4) and the upwelling along the eastern boundary (chapter 5). It is found that the thermocline variability is forced mainly by wind in a shadow zone while m~inly by surface buoyancy flux in a ventilated zone. A two-layer planetary geostrophic model is developed (chapter 2) to simulate a thermocline. The model includes some novel physical mechanisms. Most importantly, it captures the essential feature of subduction; it also is able to account for a time-varying surface temperature. The equation for the interface is a quasi-linear equation, which can be solved analytically by the method of characteristics. The effect of a varying Ekman pumping is investigated. In a shadow zone, it is found that the driving due to the Ekman pumping is mainly balanced by the propagation of planetary waves. However, in a ventilated zone, the cold advection of subducted water plays the essential role in opposing the Ekman pumping. The different dynamics also results in different thermocline variability between the two zones. After a change of Ekman pumping, in the shadow zone, since the baroclinic Ross by wave responds to a changing Ekman pumping slowly (in years to decades), an imbalance arises between the Rossby wave and the Ekman pumping, which then excites thermocline variability. However, in the ventilated zone, both the advection and the Ekman pumping vary rapidly after a barotropic process (about one week) to reach a new steady balance, leaving little thermocline variability. In addition, the evolution of the thermocline and circulation are also discussed. Furthermore, with a periodic Ekman pumping, it is found that linear solutions are approximate the fully nonlinear solution well, particularly for annual forcings. However, the linear disturbance is strongly affected by the basic thermocline structure and circulation. The divergent group velocity field, which is mainly caused by the divergent Sverdrup flow field, produces a decay effect on disturbances. The mean thermocline structure also strongly affects the relative importance of the local Ekman pumping and remote Rossby waves. As a result, in a shadow zone, local response dominates for a shallow interface while the remote Rossby wave dominates for a deep interface. With a strong decadal forcing, the nonlinearity becomes important in the shadow zone, particularly in the western part. The time-mean thermocline which results, becomes shallower than the steady thermocline under the mean Ekman pumping. Then, we investigate the effect on the permanent thermocline by a moving outcrop line, which simulates the effect of a varying surface heat flux. The two layer model is modified by adding an (essentially passive) mixed layer atop. The outcrop line and the mixed layer depth are specified. It is found that, opposite to a surface wind stress, a surface buoyancy flux causes strong variability in the ventilated zone through subducted water while it affects the shadow zone very little. Furthermore, two regimes of buoyancy-forced solution are found. When the outcrop line moves slowly, the solutions are non-entrainment solutions. For these solutions, the surface heat flux is mainly balanced by the horizontal advection. The mixed layer is never entrained. The time-mean thermocline is close to the steady thermocline with the time-mean outcrop line. When the outcrop line moves southward rapidly during the cooling season, the solutions become entrainment solutions. Now, deep vertical convection must occur, because the horizontal advection in the permanent thermocline is no longer strong enough to balance the surface cooling. The mixed layer penetrates rapidly such that water mass is entrained into the mixed layer through the bottom. The time-mean thermocline resembles the steady thermocline with the early spring mixed layer, as suggested by Stommel (1979). The local variability in the permanent thermocline is most efficiently produced by decadal forcings. Finally, two issues about the waves radiating from the eastern boundary are discussed. The first is the penetration of planetary waves across the southern boundary of a subtropical gyre. We find that the wave penetration across the southern boundary is substantially changed by the zonal variation of the thermocline structure. The zonal variation alters both the effective β and the wave front orientation. As a result, the wave penetration differs for interfaces at different depths. For an interface near the surface, part of the waves penetrate into the equatorial region. For middle depths, most waves will be trapped within the subtropical gyre. In contrast, for deep depths, all waves penetrate southward. The second issue of the eastern boundary waves mainly concerns with the breaking of planetary waves in the presence of an Ekman pumping and the associated two-dimensional mean flow. It is found that the breaking is affected significantly by an Ekman pumping and the associated mean flow. With an Ekman pumping, downwelling breaking is suppressed and the breaking time is delayed; upwelling breaking is enhanced and their times are shortened. The breaking times and positions are mainly determined by the maximum vertical perturbation speed while the intensity of the breaking front mainly depends on the amplitude of the perturbation. The intensity of a breaking front increases with the amplitude of the forcing, but decreases with the distance from the eastern boundary. The orientation of a breaking front is overall in northeast-southwest (x ~ -1/f2).

Description: This thesis is supported by National Science Foundation, Division of Atmospheric Sciences.

Description: [1]  The relative importance of tropical SST anomalies to the dominant variability of East Asian Summer Monsoon (EASM) Circulation is investigated using an atmospheric GCM and a linear inverse model. It is found that the cooling over the central tropical Pacific is crucial in developing and maintaining the summertime northwest Pacific anticyclones, associated with the EASM precipitation. In this regard, the previously suggested El Niño event in the preceding winter and accompanying tropical Indian Ocean warming alone may not be enough to predict the strength of EASM circulation. Instead, monitoring and predicting the evolution of sea surface temperature anomalies in the central tropical Pacific, especially in spring to summer, may greatly improve the prediction of EASM circulation.

Description: Aims Multiplexed immunofluorescence is a powerful tool for validating multi-gene assays and understanding the complex interplay of proteins implicated in breast cancer within a morphological context. We describe a novel technology for imaging an extended panel of biomarkers on a single, formalin-fixed paraffin embedded breast sample and evaluating biomarker interaction at a single cell level, and demonstrate proof-of-concept on a small set of breast tumours including those which co-express hormone receptors with Her2/neu and Ki-67. Methods and Results Using a microfluidic flow cell, reagent exchange was automated and consisted of serial rounds of staining with dye-conjugated antibodies, imaging, and chemical deactivation. A two-step antigen retrieval process was developed to satisfy all epitopes simultaneously, and key parameters were optimized. The imaging sequence was applied to seven breast tumours, comparing with conventional immunohistochemistry. Single-cell correlation analysis was performed with automated image processing. Conclusions We have described a novel platform for evaluating biomarker colocalization. Expression in multiplexed images is consistent with conventional IHC. Automation reduces inconsistencies in staining and positional shifts, while the fluorescent dye cycling approach dramatically expands the number of biomarkers which can be visualized and quantified on a single tissue section. This article is protected by copyright. All rights reserved.

Description: Previous studies have demonstrated that tissue kallikrein (TK) protects against cerebral ischemia injury mainly through inhibition of apoptosis via bradykinin B2 receptor (B2R). In the present study, we proposed that autophagy induction contributed to the neuroprotective mechanism of TK. To validate this hypothesis, we investigated TK-induced autophagy and its signaling mechanisms in human SH-SY5Y cells exposed to oxygen and glucose deprivation (OGD). We found that TK treatment enhanced autophagy induction, reflected by augmented LC3 conversion and Beclin1 expression, decreased p62 levels and increased mRFP-LC3 puncta formation. GFP-mRFP-LC3 adenovirus assay indicated that TK maintained autophagic flux. Moreover, bafilomycin A1 (Baf.A1) caused obvious LC3-II accumulation either in the presence or absence of TK. Autophagy inhibition by Beclin1 knockdown or Baf.A1 treatment abrogated the neuroprotective effects of TK. MEK1/2/ERK1/2 and AMPK/TSC2/mTOR signaling were induced by OGD stress and enhanced by TK. MEK/ERK inhibitor U0126 alone elevated autophagy in OGD conditions but impaired TK-induced autophagy. Blockade of AMPK/TSC2/mTOR signaling by AMPK inhibitor compound C and shRNA mediated the knockdown of AMPK α1 and TSC2 but abolished autophagy in SH-SY5Y cells exposed to OGD treated either with or without TK. Moreover, B2R expression was upregulated by OGD exposure. B2R knockdown attenuated autophagy and suppressed MEK1/2/ERK1/2 and AMPK/TSC2/mTOR signaling in OGD conditions in either the presence or absence of TK. In sum, we revealed the significance of B2R-mediated MEK/ERK and AMPK signaling in autophagy induction under OGD stress, and proposed novel mechanisms involved in the neuropotective function of TK through B2R-dependent regulation of autophagy. This article is protected by copyright. All rights reserved.

Description: The particle filter (PF) and the ensemble Kalman filter (EnKF) are two promising and popularly adopted types of ensemble-based data assimilation methods for paleoclimate reconstruction. However, no systematic comparison between them has been attempted. We compare these two uncertainty based methods in pseudo proxy experiments where synthetic seasonal mean sea surface temperature (SST) observations are assimilated. Their skills are evaluated with regards to local, hemispherically- and globally-averaged analysis error, and their ability to capture large-scale modes of variability. It is found that the EAKF (Ensemble Adjstment Kalman Filter, a variant of EnKF) performs better than the PF with only one third of the ensemble size, despite PF's theoretical superiority in allowing for non-Gaussian statistics and nonlinear dynamics. The success of the EAKF is attributed to the facts that: 1) Gaussian assumption is somewhat appropriate for this application; 2) The EAKF is less sensitive to sampling errors than the PF due to the different methodological natures. 16 members are enough to estimate accurate covariance for the EAKF, but 48 (even 96) members still underrepresent the state space of high-dimensional system for the PF. Our study highlights the importance of a large localization radius in the application of the EnKF to paleoclimate reconstruction due to the sparse proxy network, and suggests that additional techniques, such as localization or clustered particle filter, are needed to improve the PF for paleoclimate reconstruction, in addition to the simple importance resampling currently adopted by most research.

Description: [1]  In this study, we propose a generalized stability indicator L for a slowly evolving and quasi-steady Atlantic meridional overturning circulation (AMOC), which represents a feedback related to the AMOC and its associated freshwater transport within the Atlantic basin. As an improvement from previous indicators for the AMOC in equilibrium, this generalized indicator does not require a divergence-free freshwater transport in the Atlantic for a collapsed AMOC, which enables it to correctly monitor the AMOC stability through the AMOC hysteresis loop in the coupled atmosphere-ocean general circulation models (CGCMs). From the simulation, the indicator L suggests that the AMOC is in a stable regime, with single equilibrium under the present-day and the Last Glacial Maximum (LGM) climates. However, under the present-day climate, a Bering Strait (BS) closure will diminish the freshwater outflow from the North Atlantic into the Arctic as the AMOC collapses, resulting in a freshwater convergence in the Atlantic basin and making the AMOC reside in a stable collapsed state, i.e., the AMOC exhibits characteristics of multiple equilibria. Further analysis shows that the BS effect is much reduced under the LGM climate. This generalized indicator L has great implications for paleoclimate studies in understanding the abrupt climate change due to the instability of the AMOC.