Digital Commons Network^™

Mitigating Pavement Edge Drop Off, Wayne Jensen, Niles Uerling

Nebraska Department of Transportation: Research Reports

The objective of this research was to investigate and document practices currently being used by the Nebraska Department of Roads (NDOR) districts and other State DOTs to mitigate pavement edge drop off. The NDOR has developed (or borrowed) and is currently incorporating into its standard practices several procedures that significantly decrease the incidence and magnitude of pavement edge-drop off. As these practices become more fully integrated into highway reconstruction projects, pavement edge drop off is expected to decrease dramatically. Localized areas of pavement edge drop off along paved lanes with bare or vegetated shoulders were noted as posing particular problems …

Mycorrhizal Roots In A Temperate Forest Take Up Organic Nitrogen From 13c- And 15n-Labeled Organic Matter, Matthew A. Vadeboncoeur, Andrew P. Ouimette, Erik A. Hobbie

All Materials

Background and Aims

The importance of the uptake of nitrogen in organic form by plants and mycorrhizal fungi has been demonstrated in various ecosystems including temperate forests. However, in previous experiments, isotopically labeled amino acids were often added to soils in concentrations that may be higher than those normally available to roots and mycorrhizal hyphae in situ, and these high concentrations could contribute to exaggerated uptake.

Methods

We used an experimental approach in which we added ¹³C-labeled and ¹⁵N-labeled whole cells to root-ingrowth cores, allowing proteolytic enzymes to release labeled organic nitrogen at a natural rate, as …

Advancing Numerical Prediction Of Physical And Biological Processes In Long Island Sound, Ling Liu

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The occurrence and spread of hypoxia in coastal waters is known to depend strongly on nutrients, primary production, water column structure, wind and tidal mixing. Accurate prediction of the onset, intensity and areal extent of hypoxia remains a challenge. Previous modeling efforts have needed to ‘tune’ vertical mixing or phytoplankton respiration in order to obtain results that agree with field observations of dissolved oxygen (DO). We use a one-dimensional physical model coupled with a biogeochemical model to establish mechanistic links between factors involved in the evolution of seasonal hypoxia in western Long Island Sound. The coupled model includes bacterial dynamics, …

The Application Of Trajectory Analysis For An Early Warning System In Stem Courses, Un Jung Lee

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The retention of STEM (science, technology, engineering, and mathematics) majors has become a national concern. “Early warning systems†(EWS) are being developed to identify students who perform poorly early in the semester so that interventions can be implemented. The research reported here utilizes clicker scores and review quiz scores collected in every class session for the longitudinal analysis, as well as pre-course concept inventory scores and self-reported student characteristics. Pre course concept inventory scores were significantly predictive of final course grade. Student demographic characteristics had a smaller fraction of final course grade explained. The cumulative average student clicker score was …

Groundwater Nitrate Contamination Remediation Through Permeable Reactive Barriers On The Forge River, Long Island, New York, Amy Bronwan Pritt

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The Forge River on the south shore of Long Island is contaminated by nitrate. The Forge River leads into Moriches Bay. Nitrate contamination in the river leads to algal blooms, hypoxia of the river and eventually fish kills. The area surrounding the Forge River is largely residential and not sewered with the residents relying on septic systems for sewage disposal. Nitrate from even small septic systems has been found in groundwater as far as 100m down gradient. Other investigators have shown the occurrence of submarine groundwater discharge on Wills Creek, a tributary of the Forge River and my study site. …

Radium Isotopes As Tracers Of Pore Water Dynamics In Two Long Island Salt Marsh Systems, Camilo Salazar

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

A study of pore water residence time as traced by short-lived radium (Ra) isotopes (224Ra and 223Ra) was conducted on two marsh systems in the south shore of Long Island, New York. Pore water was collected in July (summer) and November-December (winter) of 2013 at depths of 20 cm and 120 cm over three-station transects from the inner marsh to the marsh edge adjacent to a tidal channel. One of the marsh systems is the Wertheim Nationals Wildlife Refuge (NWR), from which two marshes were sampled; Wertheim 1 (W1), a restored marsh, and Wertheim 2 (W2), non-restored. The second marsh …

Net N2 Fluxes In Muddy Sediments Of Great Peconic Bay: Rates, Pathways & Controls, Stuart Waugh

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Abstract of the Dissertation NET N2 FLUXES IN MUDDY SEDIMENTS OF GREAT PECONIC BAY: RATES, PATHWAYS & CONTROLS by Stuart Waugh Doctor of Philosophy in Marine and Atmospheric Sciences Stony Brook University 2015 Depending on its form, nitrogen (N) can exert a dominant control on marine productivity and ecosystem structure. Multiple geochemical processes are involved in redox transformations of nitrogen (N) in marine sediments. In coastal benthic environments, a number of abiotic and biological environmental factors control the extent to which these processes are relevant and therefore the outcomes of sedimentary N transformations. This dissertation seeks to quantify rates of …

Chemical Aging And Cloud Condensation Nuclei Activity Of Biomass Burning Aerosol Proxies In The Presence Of Oh Radicals, Jonathan Hall Slade

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Biomass burning aerosol (BBA) can adversely impact regional and global air quality and represents a significant source of organic aerosol (OA) to the atmosphere that can affect climate. Aerosol particles can alter the transfer of radiation in earth's atmosphere directly by scattering and absorbing radiation or indirectly via cloud formation. Gas-to-particle, also termed heterogeneous, oxidation reactions can significantly alter the particle's physical and chemical properties. In turn, this can lead to the degradation of biomolecular markers for air quality-related aerosol source apportionment studies, the particles' lifetime, and modify the particles' abilities to serve as cloud condensation nuclei (CCN). However, the …

Marine Acoustics And Habitat Mapping In The Peconic Estuary, Ny, Michael Patrick White

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

As coastal populations grow, there is an increasing need for better spatial management of the seafloor. Multibeam backscatter data can be a powerful tool for habitat mapping and segmenting large areas of the seabed, based on similar physical characteristics. In order to increase the effectiveness of backscatter data sets, MBES data from the Peconic Estuary, NY, is reprocessed using newly developed software. These mosaics are less noisy compared to prior results. The relationship between grain size and backscatter is found to have a good correlation in the Peconic Estuary and a simple regression is used to predict mean phi size …

Multi-Marker Linkage Disequilibrium Mapping Of Quantitative Trait Loci, Soyoun Lee

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Background: Genome-wide associations have been studied for years to infer relationships between biological traits and their underlying genetic causes, known as quantitative traits loci (QTL), in a process known as QTL mapping. Single nucleotide polymorphisms (SNPs), which are commonly used genetic markers, are usually in linkage disequilibrium (LD) with each other within a small genetic region. Both single- and double-marker-based LD mapping methods have been developed by taking advantage of LD structure. Method: In this thesis, a more general LD mapping framework with an arbitrary number of markers has been developed in order to improve LD mapping and its detection …

A Dynamic Oyster Reef Bioenergetics Model: Predictions Of Secondary Production Based On Different Restoration Scenarios, Elizabeth Gomez

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The presence of oyster reefs augments the biomass and abundance of many transient fish and crustacean species. Therefore, restoration of oyster reefs has become an increasingly common practice in coastal areas with the goal of enhancing production of transient fish. However, predicting the effect of oyster restoration on transient fish community biomass remains elusive. To address this challenge, I created a trophic bioenergetic model to understand how energy transfers in an oyster reef and assess the effects of various restoration strategies on transient fish species. The model used a set of functional groups representing organisms commonly found in an oyster …

Space Acquisition Strategies Of Zostera Marina, Bradley Thomas Furman

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Seagrasses are a diverse group of clonal marine macrophytes. Their decline in recent decades has been an alarming component of estuarine urbanization, with large portions of historical coverage lost or degraded. Understanding patterns of dispersal and recruitment within and among the remaining populations is now critical to predicting the form and pace of recovery. Working in a developing eelgrass (Zostera marina) meadow in Shinnecock Bay, we combined field manipulations, genotypic surveys and correlative analyses to understand how vegetative growth and seedling recruitment contribute to space acquisition. First, we explored clonal foraging behavior and its effect on patch growth using subterranean …

Radium Isotopes As Tracers Of Pore Water Dynamics In Two Long Island Salt Marsh Systems, Camilo Salazar

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

A study of pore water residence time as traced by short-lived radium (Ra) isotopes (224Ra and 223Ra) was conducted on two marsh systems in the south shore of Long Island, New York. Pore water was collected in July (summer) and November-December (winter) of 2013 at depths of 20 cm and 120 cm over three-station transects from the inner marsh to the marsh edge adjacent to a tidal channel. One of the marsh systems is the Wertheim Nationals Wildlife Refuge (NWR), from which two marshes were sampled; Wertheim 1 (W1), a restored marsh, and Wertheim 2 (W2), non-restored. The second marsh …

Net N2 Fluxes In Muddy Sediments Of Great Peconic Bay: Rates, Pathways & Controls, Stuart Waugh

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Abstract of the Dissertation NET N2 FLUXES IN MUDDY SEDIMENTS OF GREAT PECONIC BAY: RATES, PATHWAYS & CONTROLS by Stuart Waugh Doctor of Philosophy in Marine and Atmospheric Sciences Stony Brook University 2015 Depending on its form, nitrogen (N) can exert a dominant control on marine productivity and ecosystem structure. Multiple geochemical processes are involved in redox transformations of nitrogen (N) in marine sediments. In coastal benthic environments, a number of abiotic and biological environmental factors control the extent to which these processes are relevant and therefore the outcomes of sedimentary N transformations. This dissertation seeks to quantify rates of …

Chemical Aging And Cloud Condensation Nuclei Activity Of Biomass Burning Aerosol Proxies In The Presence Of Oh Radicals, Jonathan Hall Slade

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Biomass burning aerosol (BBA) can adversely impact regional and global air quality and represents a significant source of organic aerosol (OA) to the atmosphere that can affect climate. Aerosol particles can alter the transfer of radiation in earth's atmosphere directly by scattering and absorbing radiation or indirectly via cloud formation. Gas-to-particle, also termed heterogeneous, oxidation reactions can significantly alter the particle's physical and chemical properties. In turn, this can lead to the degradation of biomolecular markers for air quality-related aerosol source apportionment studies, the particles' lifetime, and modify the particles' abilities to serve as cloud condensation nuclei (CCN). However, the …

Space Acquisition Strategies Of Zostera Marina, Bradley Thomas Furman

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Seagrasses are a diverse group of clonal marine macrophytes. Their decline in recent decades has been an alarming component of estuarine urbanization, with large portions of historical coverage lost or degraded. Understanding patterns of dispersal and recruitment within and among the remaining populations is now critical to predicting the form and pace of recovery. Working in a developing eelgrass (Zostera marina) meadow in Shinnecock Bay, we combined field manipulations, genotypic surveys and correlative analyses to understand how vegetative growth and seedling recruitment contribute to space acquisition. First, we explored clonal foraging behavior and its effect on patch growth using subterranean …

The Application Of Trajectory Analysis For An Early Warning System In Stem Courses, Un Jung Lee

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The retention of STEM (science, technology, engineering, and mathematics) majors has become a national concern. “Early warning systems†(EWS) are being developed to identify students who perform poorly early in the semester so that interventions can be implemented. The research reported here utilizes clicker scores and review quiz scores collected in every class session for the longitudinal analysis, as well as pre-course concept inventory scores and self-reported student characteristics. Pre course concept inventory scores were significantly predictive of final course grade. Student demographic characteristics had a smaller fraction of final course grade explained. The cumulative average student clicker score was …

Modeling Platelets On Parallel Computers, Seetha Malavika Pothapragada

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Mechanical Heart Valves (MHV) provides life-saving solutions to patients suffering from cardiovascular diseases. But these devices are often plagued by non-physiological flow patterns resulting in increased shear stress conditions. This leads to platelet damage, a precursor of thromboembolism, thus impeding the device usability and demanding lifelong anticoagulation treatments. While the flow and stresses are in the micron level, the platelet behavior is at the nm level, thus presenting a major computational challenge for simulating this multiscale multi-physics modeling problem. This dissertation focuses on using parallel computers to develop a computational framework based on n-particle simulations, defined by Coarse Grained Molecular …

Antibacterial Block Copolymer Thin Films And Growth Characteristics Of Hela Cells, Prafulla Keskar

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The large number of devices used in medical applications have to be protected from microbial attacks as it leads to serious harm. Further, the current methods of tackling this problem involve using chemicals such as disinfectants which are harmful to us humans. This thesis aims to study the effectiveness of block copolymer thin films against microbes without using traditional harmful methods. We have attempted to prepare anti-bacterial thin films which can kill the bacteria using their surface morphology and thus eliminate the harm posed to us. In the second part of this thesis, we studied the growth characteristics of HeLa …

Biotinylated Self-Assembled Micelles As Potential Vehicles For Targeted Anti-Cancer Drug Delivery, Weiyi Li

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Chemotherapy is one of the most commonly used cancer treatments. However, many side effects could occur due to the non-specific bindings of extremely toxic anti-cancer drugs to healthy cells and organs. Targeted delivery has been developed to enhance the selectivity of drug delivery vehicle and minimize side effects of chemotherapy. In this study, the hydrophobically modified glycol chitosan (HGC) micelle was further modified with a biotin-avidin-biotin (B-A-B) strategy to improve the tumor-selective ability of HGC. Firstly, HGC was biotinylated either at the amine groups (NH2) or the hydroxyl groups (OH) on the chitosan main chain. Then the biotin-4-fluorescein, as a …

Breath Biomarkers Detection By Chemical Sensors, Yan Li

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Our breath is a very complex mixture of chemical compositions. Usually, the majority of our exhaled breath consists of nitrogen, oxygen, carbon dioxides, water and inert gases. The remaining small fraction of breath contains thousands of components in trace amount, including inorganic gas molecules like nitric monoxide and diverse kinds of volatile organic compounds (VOCs). The concentrations of our exhaled gases are at a relatively stable level, though minor fluctuations may occur at different time of the day and they are also linked to the body status. Sometimes, if a specific breath gas of some appears to have an abnormal …

Defect Studies And Optimization Of Cvd Grown Boron Phosphide Films On Different Substrates, Xuejing Wang

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Boron phosphide (BP), a light III-V indirect semiconductor compound with medium band gap of 2.0 eV, has emerged as a promising material with its applications in solid-state neutron technology and semiconductor devices in extreme conditions. Since bulk BP is unavailable, heteroepitaxial film growth is being attempted on various substrates including silicon, silicon carbide (4H, 6H, 3C polytypes), AlN and sapphire of different orientations to determine the best substrate for growing high quality thin films. By investigating the defects (e.g. twins and grain boundaries, threading dislocations, stacking faults, inclusions) present in the BP epilayer using synchrotron white beam X-ray topography (SWBXT), …

Stress-Assisted Grain Growth In Nanocrystalline Metals Inhibited By Grain Boundary Segregation, Yang Zhang

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Stress-assisted grain growth in nanocrystalline metals transpires collectively with a number of competing deformation mechanisms. In this study, molecular dynamics simulations of surface nanoindentation were performed to quantify the plastic strain distribution among competing mechanisms as a function of grain size and temperature during stress-assisted grain growth in nanocrystalline Ni and a Ni-1 at. % P alloy. Under identical conditions of rate and temperature in nominally the same grain size structure, stress-assisted grain growth found to be prevalent in pure nanocrystalline Ni was virtually absent in the Ni-P alloy with P enriched grain boundaries. A reduction in the deformation temperature …

The Role Of Pofut2 In Gastrulation And Axis Elongation Of The Mouse Embryo, Brian Benz

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Protein O-fucosyltransferase 2 (POFUT2) elongates Thrombospondin Type 1 Repeats (TSR) with an O-linked fucose. Forty-nine potential proteins are modified by POFUT2 in the endoplasmic reticulum. Nearly half the POFUT2 targets belong to the A Disintegrin and Metalloprotease with ThromboSpondin type-1 motifs (ADAMTS) or ADAMTS-like family of proteins. One of POFUT2’s target proteins, ADAMTS9, contains 15 TSRs and is reported to be embryonic lethal around the same time as our Pofut2 LoxP mutants. In this study, we compared the Pofut2 and Adamts9 knockout phenotypes and used tissue specific deletion of Pofut2 to define the role of Pofut2 during gastrulation. Knockout of …

A Targeted Crispr-Cas9 Screen In Aml Cells, Sam Blake Chiappone

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The genetic underpinnings of a cancer are key to understanding the etiology of the disease and thus to providing a cure, because any robust cure of the disease will need to target a therapeutic window, a gene or a group of genes that are different between the cancerous cells and the normal cells. The research shown in this thesis gives insight into the genetic causes of acute myelogenous leukemia in an attempt to find a therapeutic window for this disease. A genetic screen using CRISPR-Cas9 is designed and conducted in a cell line designated RN 2-5 that was determined to …

Cyclodextrins As Lipid Exchange Mediators To Synthesize Artificial Asymmetric Model Membranes, Brad Greenstein

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The use of cyclodextrins have shown promise to exchange lipids of model membranes in various conditions. Several types of cyclodextrins have been shown to exchange lipids in different conditions. In this study, we used Methyl-alpha cyclodextrin (MαCD) to facilitate lipid exchange between donor multilamellar vesicles (MLVs) containing brain SM and large unilamellar vesicle acceptors (LUVs) composed of POPE, POPS and cholesterol. This technique is just one of several exploring the use of cyclodextrins to manipulate artificial membranes in order to obtain asymmetry. Overview of other studies involving other types of cyclodextrin are also discussed to explain what is known about …

Class Iii Phosphoinositide 3-Kinase Vps34 In Autophagy, Endocytosis, And Nutrient-Induced Signaling, Nadia Jaber

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Vps34 is the sole member of the Class III phosphoinositide 3-kinases (PI3Ks) identified in mammals thus far. It phosphorylates phosphatidylinositol (PI) to generate PI(3)P on intracellular membranes. Previous work has suggested that Vps34 is important for the protein degradation pathways of autophagy and endocytosis, as well as nutrient-induced mTOR signaling. However, due to the pluripotent nature of available PI3K inhibitors, a clear understanding of the functions of mammalian Vps34 remains to be illustrated. To investigate the precise role of Vps34 in these processes, I have generated and characterized mice with conditional genetic ablation of Vps34. Mice with liver or heart-specific …

The Pirna Pathway In The Somatic Stem Cells Of A Regeneration-Competent Flatworm, Macrostomum Lignano, Xin Zhou

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

piRNA pathway and its central components, PIWI proteins, are essential for transposon silencing and some aspects of gene regulation. Although they predominantly function in the animal germline, increasing evidence has pointed to their involvement in somatic cells. Some flatworms possess a unique somatic stem cell system named neoblasts. These totipotent cells are the only dividing cell population thus critical for postembryonic development, adult homeostasis and the remarkable regeneration ability. In the study led by Kaja A. Wasik and me, we identify and characterize piRNAs and PIWI proteins in the emerging regenerative flatworm model, Macrostomum lignano, combining targeted gene knockdown and …

Structural Insights Into Mitochondrial Gene Expression And Disease, Kip Guja

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Mitochondria are dual membrane-bound organelles found in the cytoplasm of all eukaryotic cells. Human mitochondria contain a 16.5 kb double-stranded DNA genome that encodes thirteen essential protein subunits of the oxidative phosphorylation system, as well as the two ribosomal RNAs and 22 transfer RNAs needed to translate the thirteen messenger RNAs. Oxidative phosphorylation produces the majority of energy needed for cells to sustain life, and this process is strictly dependent on expression of the mitochondrial genome. Defects in mitochondrial gene expression are linked to many human diseases, age-related pathologies, and the aging process itself. Obtaining a more detailed understanding of …

The Role Of The Scribble Protein Complex In The Regulation Of Dendrite Formation, Bingru Sun

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

During neuronal development, the neuronal cell polarizes to specify the structures of axons and dendrites. This polarized architecture regulates the input/output functions of the neuronal cell. In my thesis, I studied the molecular mechanisms of dendrite formation. My main hypothesis was that dendrite specification results from local elevation of the cGMP signal. Soluble guanylyl cyclase (sGC) is the major enzyme for the synthesis of cGMP in the embryonic brain. I study the molecular mechanism that activates sGC and leads to dendrite specification during neuronal polarization.Scribble is a scaffold protein, part of a polarity complex that establish apical-basal polarity in epithelial …