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Recent Advances In Nearshore Wave, Circulation, And Sediment Transport Modeling, James T. Kirby

Journal of Marine Research

Significant advances in the modeling of nearshore processes have occurred over recent decades as a result of developments in both computational approaches and theoretical understanding. This review examines the present state of progress primarily from a hydrodynamics standpoint, followed by a brief discussion of applications to sediment transport and morphological evolution. Wave-averaged formulations of the wave-current interaction problem and resulting models for wave-induced currents are reviewed in order to compare and contrast radiation stress and vortex force approaches. Waveresolving approaches are then discussed, with an emphasis on the recent rapid development of 3D nonhydrostatic models and their application to a …

Forecast Errors, Goodness, And Verification In Ocean Forecasting, Gary B. Brassington

Journal of Marine Research

Verification is an essential part of the forecast process that provides guidance on the statistical behavior of the system and a framework by which a forecast can be assessed for its "goodness." Much of the framework applicable to ocean forecasting has been developed within the atmospheric community. A review of the available material is given with some commentary on its relevance in the context of ocean forecasting. A statistical theory is presented for errors in an ocean forecast system (both deterministic and ensemble) and for a number of verification metrics. Theoretical results are demonstrated with empirical models and results from …

The Effect Of A Strong Warm Winter On Subtropical Zooplankton Biomass And Metabolism, Inma Herrera, José Lopéz-Cancio, Lidia Yebra, Santiago Hernández-Léon

Journal of Marine Research

Winter 2010 was the warmest of the last 30 years in the subtropical oceanic waters north of the Canary Islands. Sea surface temperature was always above 19°C, promoting a strong stratification and preventing the expected late winter bloom. The knowledge of how planktonic organisms respond to such a warm scenario is of paramount importance to predict the effect of future ocean changes. In this study, zooplankton biomass and gut fluorescence (GF), electron transport system (ETS) activity, and aminoacyl-tRNA synthetases (AARS) activity were measured as proxies of metabolism in the oceanic waters north of the Canary Islands during the winter–spring period …

Ocean Dynamics, Gregg Jacobs, Baylor Fox-Kemper

Journal of Marine Research

Operational prediction systems must balance conflicting considerations involved in representing the widest possible range of ocean physics, limited by computational constraints. Choices must be made in prediction systems that exclude particular dynamics to enable feasible solutions within defined resources. We examine some of the basic ocean dynamics that ocean prediction systems intend to represent. The two most basic simplifications are the Boussinesq and hydrostatic. Even with these limitations, ocean models represent a vast range of physical processes, and this enables application to many problems. We examine a succinct range of basic dynamics and consider how these affect operational ocean prediction …

Observations Of The East Madagascar Current System: Dynamics And Volume Transports, Aksel Voldsund, Borja Aguiar-González, Tor Gammelsrød, Jens-Otto Krakstad, Jenny Ullgren

Journal of Marine Research

The South Equatorial Current (SEC) in the Indian Ocean bifurcates when it reaches Madagascar leading, respectively, to the North East Madagascar Current (NEMC), which contours the island flowing northwestward, and to the South East Madagascar Current (SEMC), which flows southwestward. Both branches eventually contribute to the greater Agulhas Current system and thus play a part in the global ocean circulation. In addition, these currents have important effects on the local conditions for marine life. In this study, the NEMC and the SEMC are investigated based on a comprehensive, multidisciplinary survey of the east coast of Madagascar in 2008. Results from …

Reconstructing The Recent Past Ocean Variability: Status And Perspective, Simona Masina, Andrea Storto

Journal of Marine Research

In the last two decades, climate research has benefited from the continuous development of analysis systems dedicated to operational monitoring and forecasting, which opened up the possibility of exploiting the state of the art modeling and data assimilation tools to reconstruct and study the ocean during the past decades. This activity became feasible also thanks to the increasing availability of long time series of high-quality in situ and remotely-sensed observations. Retrospective analyses (or simply reanalyses or ocean syntheses), indeed combine quality controlled reprocessed ocean observations with a state-of-the-art ocean general circulation model (OGCM) using data assimilation methods to estimate the …

The North Icelandic Jet And Its Relationship To The North Icelandic Irminger Current, Robert S. Pickart, Michael A. Spall, Daniel J. Torres, Kjetil Våge, Hedinn Valdimarsson, C. Nobre, G. W. K. Moore, Steingrimur Jonsson, Dana Mastropole

Journal of Marine Research

Shipboard hydrographic and velocity sections are used to quantify aspects of the North Icelandic Jet (NIJ), which transports dense overflow water to Denmark Strait, and the North Icelandic Irminger Current (NIIC), which imports Atlantic water to the Iceland Sea. The mean transports of the two currents are comparable, in line with previous notions that there is a local overturning cell in the Iceland Sea that transforms the Atlantic water to dense overflow water. As the NIJ and NIIC flow along the north side of Iceland, they appear to share a common front when the bottom topography steers them close together, …

A Future For Intelligent Autonomous Ocean Observing Systems, P. F.J. Lermusiaux, D. N. Subramani, J. Lin, C. S. Kulkarni, A. Gupta, A. Dutt, T. Lolla, P. J. Haley Jr., W. H. Ali, C. Mirabito, S. Jana

Journal of Marine Research

Ocean scientists have dreamed of and recently started to realize an ocean observing revolution with autonomous observing platforms and sensors. Critical questions to be answered by such autonomous systems are where, when, and what to sample for optimal information, and how to optimally reach the sampling locations. Definitions, concepts, and progress towards answering these questions using quantitative predictions and fundamental principles are presented. Results in reachability and path planning, adaptive sampling, machine learning, and teaming machines with scientists are overviewed. The integrated use of differential equations and theory from varied disciplines is emphasized. The results provide an inference engine and …

Oil Spill Forecasting (Prediction), George Zodiatis, Robin Lardner, Tiago M. Alves, Yiannis Krestenitis, Leonidas Perivoliotis, Sarantis Sofianos, Katerina Spanoudaki

Journal of Marine Research

Oil spills in the ocean are a matter of concern due to the damaging effect they can have on coastal and offshore resources. This work presents a review of present-day modeling techniques used in the mitigation of oil spills by booms, skimmers, chemical dispersants, and other equipment and the importance of the controlling parameters of these techniques. Three basic questions need to be addressed by oil spill models: (1) where the spill will move, (2) when will the spill get to the modeled endpoints, and (3) what will be its state when it arrives. The first two questions are relatively …

Coupled Ocean-Atmosphere Forecasting At Short And Medium Time Scales, Julie Pullen, Richard Allard, Hyodae Seo, Arthur J. Miller, Shuyi Chen, Luciano Ponzi Pezzi, Travis Smith, Philip Chu, José Alves, Rui Caldeira

Journal of Marine Research

Recent technological advances over the past few decades have enabled the development of fully coupled atmosphere-ocean modeling prediction systems that are used today to support short-term (days to weeks) and medium-term (10–21 days) needs for both the operational and research communities. We overview the coupling framework, including model components and grid resolution considerations, as well as the coupling physics by examining heat fluxes between atmosphere and ocean, momentum transfer, and freshwater fluxes. These modeling systems can be run as fully coupled atmosphere-ocean and atmosphere-ocean-wave configurations. Examples of several modeling systems applied to complex coastal regions including Madeira Island, Adriatic Sea, …

The Generation Of Rossby Waves And Wake Eddies By Small Islands, R. C. Musgrave, G. Flierl, T. Peacock

Journal of Marine Research

The influence of small islands on zonal geostrophic currents is examined in a two-layer configuration. An analytic solution for steady quasigeostrophic flow is derived under the assumption of no upstream influence and is validated numerically in a time-dependent quasigeostrophic model. Under these conditions solutions are the sum of two eigenmodes, which are either arrested Rossby waves or evanescent depending on background flow conditions (layer speeds, stratification, and latitude). In contrast to homogeneous flows, arrested Rossby waves in two layers can occur even when the depth mean flow is westward and can be generated both to the east and west of …

Doctors, Death, And Denial: The Origins Of Hospice Care In 20th Century America, Sarah E. Pajka

Kaplan Senior Essay Prize for Use of Library Special Collections

This essay provides insight into the social and cultural trends that led to the creation of hospice care in the United States. The essay covers the changes in treatment of death by the medical profession, from the discussion of tuberculosis sanatoriums and cancer centers in the early 1900s through the rise of medical authority, and the pivotal role of Yale School of Nursing dean Florence Wald in the 1980 opening of Connecticut Hospice, the first modern American hospice facility.

Polarization Of Cystic Fibrosis Macrophages Is Dysregulated, Evan Jacob Levy

Yale Medicine Thesis Digital Library

We hypothesize that intrinsic defects in cystic fibrosis (CF) macrophages affect their ability to adequately respond to extracellular stimuli, affecting their phenotypic response and contributing to a hyper-inflammatory state.

Peripheral blood-derived monocytes from healthy donors (HD) (n=10) as well as CF subjects (n=10) were differentiated into macrophages using RPMI media with 50 ng/mL of MCSF for 10 days. Cells were treated with 100 ng/mL of LPS plus 20 ng/mL of INF-gamma to activate the M1 phenotype or 20 ng/mL of IL-4 to activate the M2 phenotype. Cells were treated for 24 hours in preparation for RNA isolation and 3 hours …

Distribution Of Selenium In The Plume Of The Gediz River, Izmir Bay, Aegean Sea, Nihayet Bizsel, Murat V. Ardelan, Kemal C. Bizsel, Ayşin Suzal, Aylin Demirdaǧ, Deniz Y. Sarica, Eiliv Steinnes

Journal of Marine Research

Selenium (Se) variations in the water column, suspended particulate matter, and sediment through the salinity gradient, together with water-quality parameters, were investigated over four different river conditions: lowest–highest runoff and high–low production period between November 2004 and August 2005 in the plume of the Gediz River, Aegean Sea, Turkey. The drainage basin of the Gediz delta is predominantly agricultural and industrial in character. Dissolved Se exceeded the water-quality standard of 5 μg L^–1 during high flow and varied from 9.4 μg L^–1 to 0.02 μg L^–1 through the salinity gradient during the study period. Particulate Se ranged …

From Weather To Ocean Predictions: An Historical Viewpoint, Nadia Pinardi, L. Cavaleri, G. Coppini, P. De Mey, C. Fratianni, J. Huthnance, P. F. J. Lermusiaux, A. Navarra, R. Preller, S. Tibaldi

Journal of Marine Research

This paper reviews the historical development of concepts and practices in the science of ocean predictions. It begins with meteorology, which conducted the first forecasting experiment in 1950, followed by wind waves, and continuing with tidal and storm surge predictions to arrive at the first successful ocean mesoscale forecast in 1983. The work of Professor A. R. Robinson of Harvard University, who produced the first mesoscale ocean predictions for the deep ocean regions is documented for the first time. The scientific and technological developments that made accurate ocean predictions possible are linked with the gradual understanding of the importance of …

Modeling And Forecasting The “Weather Of The Ocean” At The Mesoscale, Anne Marie Treguier, Eric P. Chassignet, Arnaud Le Boyer, Nadia Pinardi

Journal of Marine Research

We present a historical perspective on ocean mesoscale variability and turbulence, from the physical basis and the first numerical models to recent simulations and forecasts. In the mesoscale range (typically, spatial scales of 100 km and time scales of a month), nonlinearity, and energy cascades were well understood in the 1970s, but the emergence of coherent vortices took place much later. New challenges have arisen with the exploration of the submesoscale regime, where frontal dynamics play a key role and the range of flow instabilities is wider than in the quasi-geostrophic regime. Special focus is placed on the interaction of …

Ocean Forecasting For Wave Energy Production, Alexis Mérigaud, Victor Ramos, Francesco Paparella, John V. Ringwood

Journal of Marine Research

There are a variety of requirements for future forecasts in relation to optimizing the production of wave energy. Daily forecasts are required to plan maintenance activities and allow power producers to accurately bid on wholesale energy markets, hourly forecasts are needed to warn of impending inclement conditions, possibly placing devices in survival mode, while wave-by-wave forecasts are required to optimize the real-time loading of the device so that maximum power is extracted from the waves over all sea conditions. In addition, related hindcasts over a long time scale may be performed to assess the power production capability of a specific …

Coupled Ocean–Atmosphere Modeling And Predictions, Arthur J. Miller, Mat Collins, Silvio Gualdi, Tommy G. Jensen, Vasu Misra, Luciano Ponzi Pezzi, David W. Pierce, Dian Putrasahan, Hyodae Seo, Yu-Heng Tseng

Journal of Marine Research

Key aspects of the current state of the ability of global and regional climate models to represent dynamical processes and precipitation variations are summarized. Interannual, decadal, and global-warming timescales, wherein the influence of the oceans is relevant and the potential for predictability is highest, are emphasized. Oceanic influences on climate occur throughout the ocean and extend over land to affect many types of climate variations, including monsoons, the El Niño Southern Oscillation, decadal oscillations, and the response to greenhouse gas emissions. The fundamental ideas of coupling between the ocean-atmosphere-land system are explained for these modes in both global and regional …

Issues In Stochastic Ocean Modeling, Cecile Penland, Antonio Navarra

Journal of Marine Research

The general theory of stochastic differential equations is presented in this chapter, including the theoretical background on how measured statistics from time series can be used to develop a stochastic parameterization. The general rules of stochastic calculus, including the important and often overlooked differences between Ito and Stratonovich calculus, are mentioned, and references are provided in which more detail may be found. We discuss how Stratonovich calculus is usually appropriate for fluid systems, whereas Ito calculus is often appropriate for data assimilation. We also discuss some common numerical pitfalls awaiting the unwary modeler, and warn against unsophisticated random number generators. …

Advanced Wave Modeling, Including Wave-Current Interaction, Alexander V. Babanin, Andre Van Der Weshuijsen, Dmitry Chalikov, W. Erick Rogers

Journal of Marine Research

The paper outlines principles of phase-resolving and phase-average wave models, with emphasis on the state of the art of wave-current interaction physics. We argue that these interactions are the least well-developed part of such models. Linear and nonlinear dynamics of waves on currents are discussed; depth-integrated and depth-varying approaches are described. Finally, examples of numerical model performance for waves on currents in realistic oceanic scenarios are presented.

Tidal Prediction, Gary D. Egbert, Richard D. Ray

Journal of Marine Research

Tides are the most predictable of oceanographic phenomena, due both to the simplicity and predictability of the astronomical forcing and to the near linearity of the ocean's dynamical response. In the classical and simplest scenario, tidal prediction is based on harmonic analysis of past measurements at a fixed location. Limits to predictability arise because isolated astronomical spectral lines are broadened into "cusps" of incoherent energy, for example through interactions with non-tidal flows. Tidal prediction at locations without past measurements has historically been a major challenge, but, owing to near-global observations of modern satellite altimeters, the empirical harmonic approach now yields …

Modeling And Forecasting Ocean Acoustic Conditions, Timothy F. Duda

Journal of Marine Research

Modeling acoustic conditions in an oceanic environment is a multiple-step process. The environmental conditions (features) in the area first must be measured or estimated; relevant features include seabed geometry, seabed composition, and four-dimensionally (4D) variable sound-speed and density variations related to evolving or wave motions. Often the dynamical wave modeling depends on first obtaining correct seabed and mean stratification conditions (for example, nonlinear internal wave modeling). Next, this information must be included in sound propagation modeling. A selection of the many methods and tools available for these tasks are described, with a focus on modeling sounds of 20 to 1000 …

Aabw-Transport Variation And Its Effect On Internal Wave Motions Between Top And Bottom Of The Puerto Rico Trench, Hans Van Haren

Journal of Marine Research

Slow subinertial variations in Antarctic Bottom Water (AABW) are investigated interacting with internal waves and associated turbulent mixing in the Puerto Rico Trench (PRT), northwest Atlantic. Just below the PRT's top at 5,500 m, a deep-sea mooring was deployed for 14 months. Around 6,100 m, the line held a 200 m long string of 101 high-resolution temperature sensors and a current meter. Around 8,250 m, a similar string held 102 sensors, of which the lowest was 9 m above the bottom. As was measured with shipborne conductivity-temperature-depth profiling down to 7,150 m, PRT waters are very weakly stratified, with local …

Measurement And Modeling Of Volume Scattering Functions For Phytoplankton From Norwegian Coastal Waters, Endre Marken, Nicolausi Ssebiyonga, Jon K. Lotsberg, Jakob J. Stamnes, Børge Hamre, Øyvind Frette, Arne Skodvin Kristoffersen, Svein Rune Erga

Journal of Marine Research

The volume scattering function (VSF) describes the angular distribution of scattered light, and the VSF of phytoplankton is one of the most important inherent optical properties of oceanic water. Despite its importance, relatively few measurements of the VSF have been carried out in aquatic environments, and we present here data and analyses of measured VSFs at 442, 490, and 550 nm for 15 representative phytoplankton species from Norwegian coastal waters. In addition, the analytic scattering phase functions Henyey-Greenstein (HG) and Fournier-Forand, as well as Mie theory, were fitted and compared to the measured VSFs. The measured VSFs for all the …

Numerical Modelling In A Multiscale Ocean, Dale B. Haidvogel, Enrique N. Curchitser, Sergey Danilov, Baylor Fox-Kemper

Journal of Marine Research

Systematic improvement in ocean modelling and prediction systems over the past several decades has resulted from several concurrent factors. The first of these has been a sustained increase in computational power, as summarized in Moore's Law, without which much of this recent progress would not have been possible. Despite the limits imposed by existing computer hardware, however, significant accruals in system performance over the years have been achieved through novel innovations in system software, specifically the equations used to represent the temporal evolution of the oceanic state as well as the numerical solution procedures employed to solve them. …

Coupled Ice-Ocean Modeling And Predictions, Laurent Bertino, Marika M. Holland

Journal of Marine Research

We review the coupled ice-ocean modeling activities aimed at predictions, both in the near term (days to a week) and in the long term (seasonal to decadal) of the polar oceans. First the state of the knowledge of potential predictability is exposed, then an overview is given of the tools available for carrying out such predictions: the observations that can be used to initialize actual predictions, the coupled ice-ocean–modeling, including the fully-coupled Earth System Models for long-term predictions, and data-assimilation techniques. Finally, the performance of existing prediction systems is reviewed, showing that, although more predictive capability remains than what is …

An Idh1 Mutation Prevalent In Glioma Confers Deficient Dna Repair And Sensitivity To Parp Inhibition, Nathaniel David Robinson

Yale Medicine Thesis Digital Library

High-grade gliomas (HGGs) are devastating malignancies of the central nervous system, and few treatment options are available for these tumors. In the most malignant form of the disease, glioblastoma multiforme (GBM), over 90% of patients will succumb to their tumor within 5 years after standard of care treatment, consisting of surgery, radiation therapy, and temozolomide chemotherapy. It is now clear that gliomas are molecularly heterogeneous entities, with mutations in tumor suppressors and oncogenes defining many distinct sub-types with important therapy implications. However, almost all HGGs are treated with a limited array of initial therapies, regardless of these molecular differences. Isocitrate …

Differentiation Control In Tissue-Engineered Vascular Grafts With Oxygen & Small Molecule Inhibitors, Joshua Morgan Arthur Siewert

Yale Medicine Thesis Digital Library

Tissue-engineered vascular grafts (TEVGs) have the potential to provide life-saving arterial replacements to patients requiring vascular bypass, hemodialysis access, and pediatric coronary surgery. Recent years have seen impressive strides towards widespread clinical use, but significant work still remains in optimizing cell source and graft growth, including the suppression of unwanted calcification during culture.

In this study, I examine oxygen concentration and two small-molecule bone morphogenic protein (BMP) inhibitors, DMH-1 and LDN193189, as potential avenues of increased control over mesenchymal stem cell (MSC) differentiation of into vascular smooth muscle cells (SMCs). Applying BMP-inhibitor concentrations from 0.01 to 10 µM at oxygen …

Yale School Of Medicine Facts & Figures 2017-2018, Yale School Of Medicine Office Of Communications

Facts & Figures – annual Yale School of Medicine numbers

Provided by the Office of Communications, the Facts and Figures brochure is produced annually as a way to provide a snapshot of key facts and data related to the School of Medicine as well as the Medical Campus. This includes enrollment data, research activity, financial summaries, and more.

Genetics Of Chemotherapy Response In Triple Negative Breast Cancer, Charles Li

Yale Medicine Thesis Digital Library

Triple Negative Breast Cancer (TNBC) encompasses a wide range of treatment responses, however there are no predictive biomarkers approved for clinical use to target therapy. With a novel exome analysis method, we discovered that the overall proportion of the homologous recombination repair (HRR) genes affected by structural variation can accurately predict both positive and negative chemotherapy response prior to initiation of therapy in the large majority of patients in our cohort.

We analyzed exome sequences of unpaired tumor samples, collected prior to ACT chemotherapy, in 17 TNBC patients who exhibit complete pathologic response to neoadjuvant chemotherapy (pCR) and 15 patients …