Digital Commons Network^™

Vortex Competition In Coastal Outflows, Sean Jamshidi, Edward Johnson

Journal of Marine Research

Experiments and field observations have shown that there are at least two modes of behavior for river plumes. In many cases, the plume turns to the right (in the Northern Hemisphere) on leaving the river mouth and follows the direction of Kelvin-wave propagation. Alternatively, a “bulge” can form in the plume and a fraction of the outflow volume becomes trapped near the mouth. This paper discusses how bulge formation can be affected by the vorticity profile at the river mouth. Due to the image effect, regions of cyclonic vorticity tend to propagate rightwards, whereas regions of anticyclonic vorticity propagate leftward …

The Regulation Of Oxygen To Low Concentrations In Marine Oxygen-Minimum Zones, Don E. Canfield, Beate Kraft, Carolin R. Löscher, Richard A. Boyle, Bo Thamdrup, Frank J. Stewart

Journal of Marine Research

The Bay of Bengal hosts persistent, measurable, but sub-micromolar, concentrations of oxygen in its oxygen-minimum zone (OMZ). Such low-oxygen conditions are not necessarily rare in the global ocean and seem also to characterize the OMZ of the Pescadero Basin in the Gulf of California, as well as the outer edges of otherwise anoxic OMZs, such as can be found, for example, in the Eastern Tropical North Pacific. We show here that biological controls on oxygen consumption are required to allow the semistable persistence of low-oxygen conditions in OMZ settings; otherwise, only small changes in physical mixing or rates of primary …

Advancing Science From Plankton To Whales—Celebrating The Contributions Of James J. Mccarthy, Patricia M. Glibert, Mark A. Altabet, Joseph P. Montoya, Dennis J. Mcgillicuddy Jr.

Journal of Marine Research

Hailing from Sweet Home, Oregon, where his father introduced him to the fascinations of pondwater (McCarthy 2018), Jim McCarthy graduated from Gonzaga University, and in the late 1960s joined the Food Chain Research Group at the Scripps Institution of Oceanography, where he received his doctorate in 1971. The Food Chain Research Group, which was becoming recognized as the premier research group on plankton, was at that time directed by such distinguished scientists as John Strickland and Dick Eppley, among others. The goal of the Food Chain Group was to understand plankton dynamics and trophodynamics, “to a degree that will enable …

Urea Uptake And Urease Activity In The Chesapeake Bay, Caroline M. Solomon

Journal of Marine Research

The importance of urea in supplying the nitrogen (N) required by planktonic communities has long been recognized, notably by James J. McCarthy in studies as early as the 1970s. Utilization of urea involves a two-step enzymatic process in phytoplankton, with urea first entering the cell via transport (i.e., urea uptake), followed by the conversion of urea into ammonium by the enzyme urease. This article describes a series of field observations and experiments conducted in the Chesapeake Bay, USA, from 2001 through 2018, aimed at understanding the relationship between urea uptake and urease activity and the role of environmental factors on …

N-Loss Stoichiometry In A Peru Odz Eddy, Mark A. Altabet, Annie Bourbonnais

Journal of Marine Research

Assuming heterotrophic denitrification as the dominant microbial process, Richards (1965) formulated a stoichiometry governing nitrogen loss in open-ocean oxygen deficient zones (ODZs). It prescribes the quantitative coupling between the oxidation of organic matter by NO^–₃ in the absence of O₂ and the corresponding production of CO₂, N₂, and PO^–3₄. Applied globally, this relationship defines key linkages between the C, N, and P cycles. However, the validity of Richards's stoichiometry is challenged by recognition of complex microbial N processing in ODZs including anammox as an important pathway and nitrite reoxidation. Whereas …

The Wave-Current Interaction In The Coastal Area, Homayoon Komijani, Jaak Monbaliu

Journal of Marine Research

In our investigation of the effect of wind-waves on barotropic mean flow in coastal areas, we compare two methods for calculating wave-induced force. The wave field is simulated by the nearshore spectral wave model SWAN. The wave-induced force (calculated using the radiation stress gradient and dissipation methods) and the Stokes drift are integrated in the COHERENS circulation model in the depth-averaged mode. The coupled set is validated using well-known academic test cases of planar beach and single-barred beach. Finally, in a two-dimensional test case based on Belgian coastal waters we compare simulations of mean flow using the two methods of …

Comparing Apples To Oranges: Perspectives On Satellite-Based Primary Production Estimates Drawn From A Global Biogeochemical Model, Charles A. Stock

Journal of Marine Research

Net primary production (NPP) by microscopic phytoplankton underpins nearly all marine life, yet global NPP estimates differ substantially. Among satellite-based estimates, variation has been attributed to differing assumptions about the relationships between photosynthesis and sea surface temperature (SST). Maximum chlorophyll (Chl)–specific rates of carbon fixation in the water column (P^B_opt) increase monotonically with SST in some satellite algorithms, whereas others peak at intermediate values. Understanding and constraining such relationships is challenged by the many direct and indirect relationships between temperature and phytoplankton. In this article, the emergent P^B_opt-SST relationship was diagnosed in a …

Deep Circulation In The Lau Basin And Havre Trough Of The Western South Pacific Ocean From Floats And Hydrography, Elizabeth Simons, Kevin Speer, Andreas M. Thurnherr

Journal of Marine Research

A system of meridional ridges in the western South Pacific Ocean frame the Lau Basin and Havre Trough, and form a barrier to direct communication between the far western South Pacific basins and the interior South Pacific Ocean. The eastern side of this system comprises the Tonga and Kermadec Ridges, the location of the main deep western boundary current entering the Pacific Ocean. Observations from floats released in the Lau Basin as part of the RIDGE2000 program suggested the presence of a western boundary current along the Lau Ridge exiting into the North Fiji Basin. Those observations, together with Argo …

Phytoplankton In The Aqueous Ecological Theater: Changing Conditions, Biodiversity, And Evolving Ecological Concepts, Patricia M. Glibert

Journal of Marine Research

Phytoplankton communities, from lakes to oceans, are changing with anthropogenic nutrient loading and climate change. So, too, are the tools by which phytoplankton are quantified and characterized, yielding a torrent of new data and new types of data that can be related to ecosystem function. New insights have been gained about the physiology of resource acquisition by phytoplankton, allowing new relationships between phytoplankton biodiversity and function to be developed. Despite years of emphasis on the use of inorganic substrates in support of phytoplankton nutrition, it is now well understood that phytoplankton rely on a broad suite of substrates, both dissolved …

A Metapopulation Model For Whale-Fall Specialists: The Largest Whales Are Essential To Prevent Species Extinctions, Craig R. Smith, Joe Roman, J. B. Nation

Journal of Marine Research

The sunken carcasses of great whales (i.e., whale falls) provide an important deep-sea habitat for more than 100 species that may be considered whale-fall specialists. Commercial whaling has reduced the abundance and size of whales, and thus whale-fall habitats, as great whales were hunted and removed from the oceans, often to near extinction. In this article, we use a metapopulation modeling approach to explore the consequences of whaling to the abundance and persistence of whale-fall habitats in the deep sea and to the potential for extinction of whale-fall specialists. Our modeling indicates that the persistence of metapopulations of whale-fall specialists …

Estimating Particle Export Fl Ux From Satellite Observations: Challenges Associated With Spatial And Temporal Decoupling Of Production And Export, Dennis J. Mcgillicuddy Jr., Laure Resplandy, Marina Lévy

Journal of Marine Research

Recent studies have suggested that accurate predictions of particle export flux can be derived from satellite-based estimates of phytoplankton biomass and net primary production (NPP), combined with models of the food web. We evaluate the performance of this approach using the output of a highresolution, basin-scale coupled physical-biogeochemical model. There is tight correlation between the annual mean export flux simulated by the biogeochemical model and that predicted by the satellitebased algorithm driven by NPP from the model. Although the satellite-based approach performs well on the annual average, there are significant departures during the course of the year, particularly in spring. …

Controlling Pregnancy: Fred Lyman Adair And The Influence Of Eugenics On The Development Of Prenatal Care, Florence Hsiao

Yale Medicine Thesis Digital Library

This thesis examines the development of prenatal care in the United States in the early 1900s by focusing on the life and career of Fred Lyman Adair who, as an obstetrician and eugenicist, played a significant role in shaping prenatal care into what it is today. Although prenatal care was a product of infant welfare activists and public health officials, obstetricians like Adair who struggled to establish obstetrics as a legitimate specialty, saw an opportunity in prenatal care to pathologize pregnancy and elevate their specialty. Adair, therefore, became one of the foremost champions of prenatal care, and helped to standardize …

Multimodal Imaging And Asymmetry Of Disease Progression In Rhodopsin-Associated Autosomal Dominant Retinitis Pigmentosa, Lawrence Chan

Yale Medicine Thesis Digital Library

Retinitis pigmentosa (RP) is a group of genetically and clinically heterogeneous inherited retinal degenerative diseases with no known cure to date. The recent gene therapy treatment for Leber’s congenital amaurosis and RP caused by mutations in RPE65 have resulted in dramatic improvements in vision, leading to excitement for other potential gene therapies on the horizon. Upcoming clinical trials will be targeting patients with specific mutations, and measurements of disease progression will be needed for each genetic subtype of RP in order to determine whether treatments are successful. In this retrospective cohort study, we examined 27 RP patients with confirmed autosomal …

Development Of Pancreatic Cancer Organoid Model For Studying Immune Response In Pancreatic Cancer, Jin Woo Yoo

Yale Medicine Thesis Digital Library

The importance of immune system in pancreatic ductal adenocarcinoma (PDAC) pathogenesis and therapy remains poorly understood largely due to the lack of effective model systems. Cell lines are not physiologic as they cannot recapitulate the cancer stroma and lose genetic heterogeneity over time. Genetically engineered mouse models of PDAC are more physiologic than cell lines but lack neoantigens needed to mount T cell responses against tumor. Organoid models of PDAC offer unique opportunity to study immune mechanisms in PDAC since organoids can model complex layering of multiple cell types, creating a physiologically relevant system that is highly tractable for genetic …

The Medial Prefrontal Cortex To Dorsal Raphe Circuit In The Antidepressant Action Of Ketamine, Alexandra Thomas

Yale Medicine Thesis Digital Library

Major depressive disorder is a common and debilitating illness for which there is a notable lack of efficient, effective treatment. While currently available pharmacotherapies typically take eight weeks to take effect and fail to do so at all for about a third of patients, the N-methyl-D-aspartate (NMDA) receptor antagonist ketamine has shown a much more favorable effectiveness profile, including improvements in symptoms within hours of administration, even for many patients who do not respond to typical antidepressants. Ketamine, as a modulator of glutamate signaling in the brain, has a distinct mechanism of action from the serotonin and norepinephrine modulators that …

Impact Of Fdaaa On Registration, Results Reporting, And Publication Of Clinical Trials Evaluating New Neuropsychiatric Drugs Approved Between 2005 And 2014, Constance Xuanyi Zou

Yale Medicine Thesis Digital Library

Evidence-based medicine (EBM) promotes the use of randomized controlled trials (RCTs) published in peer reviewed medical journals as the “gold standard”. However, up to 50% of the completed clinical trials are never published and trials with results in favor of studied interventions are 2-4 times more likely to have been published then those with non favorable results. Publication bias seems to be a particularly severe problem for RCTs evaluating newly approved brand-name neuropsychiatric drugs. Mandatory trial registration, and later results reporting, were proposed to mitigate selective clinical trial publication and outcome reporting. Congress enacted the FDA Amendments Act (FDAAA) on …

Influence Of Medicare Formulary Restrictions On Evidence-Based Prescribing Practices, Aishwarya Vijay

Yale Medicine Thesis Digital Library

Controlling the cost of prescription drugs is integral to improving health outcomes, and patient access and adherence to treatment. While prescription drugs can often provide essential therapeutic benefit, previous studies have suggested that inappropriate prescription drug use is a principal cause of adverse drug events as well as abuse and diversion of drugs. Thus, balancing the benefits and harms to promote appropriate prescription drug use is an essential component of healthcare delivery in the United States. There are multiple ways appropriate prescription drug use is promoted. Black-box warnings and drug labeling controlled by the FDA as well as guidelines released …

Identifying Quantitative Enhancement-Based Imaging Biomarkers In Patients With Colorectal Cancer Liver Metastases Undergoing Loco-Regional Tumor Therapy, Mansur Abdul Ghani

Yale Medicine Thesis Digital Library

The purpose of this study was to test and compare the ability of radiologic measurements of lesion diameter, volume, and enhancement on baseline magnetic resonance (MR) images to be predictors of overall survival (OS) and markers of treatment response in patients with liver-dominant colorectal cancer metastases undergoing loco-regional tumor therapies.

This retrospective study included 88 patients with colorectal cancer (CRC) liver metastases, treated with transarterial chemoembolization (TACE) or Y90 transarterial radioembolization (TARE) between 2001 and 2014. All patients received contrast-enhanced MRI prior to therapy. Semi-automated whole liver and tumor segmentations of three dominant lesions were performed on baseline MRI to …

The Genetics Of Vein Of Galen Malformation And Assessment Of Candidate Genes In Xenopus Tropicalis, Jonathan Read Gaillard

Yale Medicine Thesis Digital Library

The Vein of Galen Malformation (VOGM) is a specific subtype of arteriovenous malformation (AVM) that becomes evident in weeks 6-11 of embryonic development. VOGM comprise less than 1% of all vascular malformations, yet represent 30% of all pediatric intracranial vascular malformations. Depending on their specific characteristics, i.e. its feeding vessels, it can present clinically as devastating congestive heart failure in neonates, hydrocephalus in children, or seizures and headaches in young adults. Advances in treatment provide improved survival, primarily through endovascular surgery. The genetic and molecular etiology of VOGM remains relatively unknown, with the only associated genes being in the context …

Outcomes Of Human Papillomavirus-Associated Head And Neck Cancers, Hong Li

Yale Medicine Thesis Digital Library

Head and neck cancers are the 6th most common solid cancer in the world. Human papillomavirus (HPV) infections are now accepted to be a previously unrecognized causative agent for head and neck squamous cell carcinomas (HNSCCs). However, research surrounding HPV’s effect at non-oropharynx sub-site is limited. There is also mixed literature over the prognostic effect of patient sex and age on overall survival in HNSCCs. We sought to utilize the National Cancer Database from 2004-2013 to evaluate the outcomes of the aforementioned objectives. Univariate and multivariate survival analyses were conducted with chi-square tests, Kaplan-Meier estimates, log-rank tests, and Cox proportional …

Home Visits In Internal Medicine Graduate Medical Education, Amitte Rosenfeld

Yale Medicine Thesis Digital Library

Home-based care training is largely absent from internal medicine (IM) graduate medical education, and home-based care program evaluation largely focuses on resident attitudes and satisfaction, rather than impact on practice or the patient experience. In the 2015-16 academic year, the Yale Primary Care Internal Medicine residency program (YPC) incorporated required home visits for all PGY-1s and PGY-2s. These visits are intended to build unique clinical skillsets, enhance education about the role of psychosocial determinants of health, and potentially impact resident wellbeing. A qualitative method was used to evaluate this program with the goal of characterizing the impact of one-time home …

A Report Of Us Physicians’ Beliefs About Physician-Assisted Suicide And A Bioethical Analysis Of The Practice, Peter Theodore Hetzler

Yale Medicine Thesis Digital Library

A REPORT OF US PHYSICIANS’ BELIEFS ABOUT PHYSICIAN-ASSISTED SUICIDE AND A BIOETHICAL ANALYSIS OF THE PRACTICE.

Peter T. Hetzler III, James Nie, Amanda Zhou, and Lydia S. Dugdale. Department of Internal Medicine, Yale University, School of Medicine, New Haven, CT.

The goals of this work were two fold. The first was to assess the beliefs of US physicians about the national legalization of physician-assisted suicide (PAS). The second was to determine the moral permissibility of PAS through a bioethical analysis. For the former, we sent a survey to 1000 randomly chosen physicians from around the US. For the last, we …

Drumming To Communicate Emotion: Dual-Brain Imaging Informs An Intervention In A Carceral Setting, Rahil Rojiani

Yale Medicine Thesis Digital Library

Drumming is an ancient nonverbal communication modality for expression of emotion. However, there has been limited exploration of its possible applications in clinical settings. Further, the underlying neural systems engaged during live communication with drumming have not been identified. We investigated the neural response to live, natural communication of emotion via drumming using a novel dual-brain neuroimaging paradigm to discover its unique neurophysiological mechanisms related to drum behavior and cross-brain coherence, and as compared to talking. We then investigated the application of a drumming intervention in an incarcerated, halfway house population to characterize intervention feasibility, elucidate the phenomenology of social …

Recirculating Flow In A Basin With Closed F/H Contours, Alexander M. Fuller, Thomas W. N. Haine, Erik Kvaleberg

Journal of Marine Research

A general circulation model is used to study the time evolution of a rotating, weakly baroclinic fluid in a basin with sloping sidewalls. Contours of f/h, where f is the Coriolis parameter and h is the depth of the fluid, are closed in this model. The fluid is forced by a localized source of positive vorticity. The initial response is a narrow, recirculating cell that resembles a β-plume modified by bathymetry. Such cells have been found in previous studies and have been linked to the recirculation cells observed in the subpolar North Atlantic. However, this is not a steady …

Jim Mccarthy’S Achievements At The Intersection Of Science With Public Policy, John P. Holdren

Journal of Marine Research

Along with his distinguished research career as a biological oceanographer and marine biologist and his inspiring service as a teacher, advisor, and mentor to students and junior colleagues at Harvard University, Jim McCarthy has been a scientific statesman of the first order, bringing insights from his research and his deep understanding of the role of science in society into the arenas of management of scientific enterprises and public and policy-maker education about the science relating to some of the greatest challenges of our time. His roles at the intersection of science with public issues have included stints as director of …

Hats Off To You, Jim!, Bill Boicourt, Doug Capone, Ed Carpenter, Penny Chisholm, Paul Falkowski, Jim Galloway, Dave Kirchman, Fred Lipschultz, Hal Mooney, François Morel, John Nevins, Mike Roman, Dan Schrag, Sybil Seitzinger, Bess Ward

Journal of Marine Research

Jim’s intellectual curiosity was an inspiration. In addition to those whose comments follow, he clearly touched the careers and lives of many others.

The Microbial Loop Concept: A History, 1930–1974, Peter J. Le B. Williams, Hugh W. Ducklow

Journal of Marine Research

The microbial loop as a leading concept in marine microbiology gained wide recognition in the 1980s, but it has roots extending back to the 1930s when microbiologists first began to take a more dynamic approach to investigating the roles of bacteria in ocean food webs and biogeochemical cycles. Here we present a history of the microbial loop concept with emphasis on the period starting in 1930, when marine bacteriologists in Russia and the West began to study explicitly the roles of marine bacteria in the sea. Selman Waksman at Woods Hole and Claude ZoBell at La Jolla relied on colony …

The Ecological And Biogeochemical State Of The North Pacifi C Subtropical Gyre Is Linked To Sea Surface Height, Benedetto Barone, Ashley R. Coenen, Stephen J. Beckett, Dennis J. Mcgillicuddy Jr., Joshua S. Weitz, David M. Karl

Journal of Marine Research

Sea surface height (SSH) is routinely measured from satellites and used to infer ocean currents, including eddies, that affect the distribution of organisms and substances in the ocean. SSH not only reflects the dynamics of the surface layer, but also is sensitive to the fluctuations of the main pycnocline; thus it is linked to events of nutrient upwelling. Beyond episodic upwelling events, it is not clear if and how SSH is linked to broader changes in the biogeochemical state of marine ecosystems. Our analysis of 23 years of satellite observations and biogeochemical measurements from the North Pacific Subtropical Gyre shows …

Brink: A Review Of Books, Issue 4, Daniel Yadin, Claire Elliman, Bix Archer, Gabriel Groz, Ruby Bilger, Oriana Tang

Brink

No abstract provided.

Bioaccumulation Of Heavy Metals In Mesozooplankton From A Human-Impacted South Western Atlantic Estuary (Argentina), Diana M. Villagran, Melisa D. Fernández Severini, Florencia Biancalana, Carla V. Spetter, Eleonora M. Fernández, Jorge E. Macrovecchio

Journal of Marine Research

The total metal concentrations (Cd, Cu, Pb, Zn, Mn, Ni, Cr, and Fe) in the mesozooplankton (200 μm–2 mm) were studied for a year in a human-impacted estuary strongly affected by urban and industrial discharges located in the South Atlantic. Over the last 25 years, this estuary has been the site of significant anthropogenic impacts including industrial activities, maritime traffic, and regular dredging. A quantitative and qualitative analysis was also carried out to identify the mesozooplanktonic community that was sampled for metal determinations. The mesozooplankton had high concentrations of toxic metals such as Cd, Pb, Cr, and Ni, which may …