AN INVESTIGATION INTO THE ANALYTICAL UTILITY OF CHANGES IN POLARIZATION ACCOMPANYING ANALYTICAL DERIVATIZATION REACTIONS (FLUORESCENCE)

Derivatization reactions between amines, alcohols and carbonyl groups with various reagents were studied. The goal of the work discussed in this dissertation was to generate basic data to know whether and in what context changes in fluorescence polarization are useful for following analytical derivatization reactions. Reactions between primary amines and fluorescein isothiocyanate were initially studied. Changes in polarization were observed upon conjugation for many of the amines primarily due to changes in fluorescence lifetime. This reaction was also studied in varying amounts of glycerol to judge the effect of glycerol on the reaction rate. Optimum percentages of glycerol were determined. Rate data of reactions of fluorescein isothiocyanate with aniline and p-chloroaniline are reported. Reactions between amines and alcohols with dichlorotriazinyl fluorescein were studied next. Minimal changes in polarization were observed upon conjugation because the lifetimes were very similar to that of the reagent. Glycerol was a problem as it reacts rapidly with the reagent. In a set of kinetics experiments with polyethyleneimine, changes in polarization were observed but could not be distinguished from randomness brought about by the experimental conditions. Dansyl chloride was more difficult to work with than either of the fluorescein compounds due to its sensitivity to environment. This was illustrated by dramatic changes in lifetime as the amount of glycerol in the solution was varied for Perrin plots. The final study involved dansyl hydrazine and reactions with carbonyls. Polarizations again changed upon conjugation due to lifetime changes. Spectral shifts were also noted upon conjugation to two carbonyl compounds. Rate data for reactions with anisaldehyde are reported. A different TLC solvent system is suggested for separation of conjugate and free dansyl hydrazine

Observation of High-Energy Astrophysical Neutrinos in Three Years of IceCube Data

A search for high-energy neutrinos interacting within the IceCube detector between 2010 and 2012 provided the first evidence for a high-energy neutrino flux of extraterrestrial origin. Results from an analysis using the same methods with a third year (2012-2013) of data from the complete IceCube detector are consistent with the previously reported astrophysical flux in the 100 TeV - PeV range at the level of $10^{-8}\, \mathrm{GeV}\, \mathrm{cm}^{-2}\, \mathrm{s}^{-1}\, \mathrm{sr}^{-1}$ per flavor and reject a purely atmospheric explanation for the combined 3-year data at $5.7 \sigma$. The data are consistent with expectations for equal fluxes of all three neutrino flavors and with isotropic arrival directions, suggesting either numerous or spatially extended sources. The three-year dataset, with a livetime of 988 days, contains a total of 37 neutrino candidate events with deposited energies ranging from 30 to 2000 TeV. The 2000 TeV event is the highest-energy neutrino interaction ever observed.Comment: 8 pages, 5 figures. Accepted by PRL. The event catalog, event displays, and other data tables are included after the final page of the article. Changed from the initial submission to reflect referee comments, expanding the section on atmospheric backgrounds, and fixes offsets of up to 0.9 seconds in reported event times. Address correspondence to: J. Feintzeig, C. Kopper, N. Whitehor

Computation of Steady-State Probability Distributions in Stochastic Models of Cellular Networks

Cellular processes are “noisy”. In each cell, concentrations of molecules are subject to random fluctuations due to the small numbers of these molecules and to environmental perturbations. While noise varies with time, it is often measured at steady state, for example by flow cytometry. When interrogating aspects of a cellular network by such steady-state measurements of network components, a key need is to develop efficient methods to simulate and compute these distributions. We describe innovations in stochastic modeling coupled with approaches to this computational challenge: first, an approach to modeling intrinsic noise via solution of the chemical master equation, and second, a convolution technique to account for contributions of extrinsic noise. We show how these techniques can be combined in a streamlined procedure for evaluation of different sources of variability in a biochemical network. Evaluation and illustrations are given in analysis of two well-characterized synthetic gene circuits, as well as a signaling network underlying the mammalian cell cycle entry

Measurement of atmospheric neutrino oscillations with IceCube

We present the first statistically significant detection of neutrino oscillations in the high-energy regime (>20 GeV) from an analysis of IceCube Neutrino Observatory data collected in 2010 and 2011. This measurement is made possible by the low-energy threshold of the DeepCore detector (~20 GeV) and benefits from the use of the IceCube detector as a veto against cosmic-ray-induced muon background. The oscillation signal was detected within a low-energy muon neutrino sample (20-100 GeV) extracted from data collected by DeepCore. A high-energy muon neutrino sample (100 GeV-10 TeV) was extracted from IceCube data to constrain systematic uncertainties. The disappearance of low-energy upward-going muon neutrinos was observed, and the nonoscillation hypothesis is rejected with more than 5σ significance. In a two-neutrino flavor formalism, our data are best described by the atmospheric neutrino oscillation parameters |Δm(32)(2)|=(2.3(-0.5)(+0.6))×10(-3) eV(2) and sin(2)(2θ(23))>0.93, and maximum mixing is favored.M. G. Aartsen ... G. C. Hill ... et al. (IceCube Collaboration

Measurement of the cosmic ray energy spectrum with IceTop-73

We report on the measurement of the all-particle cosmic ray energy spectrum with the IceTop air shower array in the energy range from 1.58 PeV to 1.26 EeV. The IceTop air shower array is the surface component of the IceCube Neutrino Observatory at the geographical South Pole. The analysis was performed using only information from IceTop. The data used in this work were taken from June 1, 2010 to May 13, 2011. During that period the IceTop array consisted of 73 stations, compared to 81 in its final configuration. The measured spectrum exhibits a clear deviation from a single power law above the knee around 4 PeV and below 1 EeV. We observe spectral hardening around 18 PeV and steepening around 130 PeV.M. G. Aartsen ... G. C. Hill ... et al. (IceCube Collaboration

Drinking Before the Drills: a Study of Three Pristine Water Sites in Sullivan County

During the last decade, technologies have improved allowing for extraction of natural gas from the Marcellus shale at depths of eight to ten thousand feet, opening Pennsylvania for drilling and fracking. Economic reality, however, has caused oil and gas companies to delay drilling at many of the sites for which they have obtained drilling permits. This affords us the opportunity to measure natural non-impacted chemical quantities (aka baseline data) at several ponds in Sullivan County, specifically Sones Pond, Beech Lake, and Shumans Lake. Sones Pond is located in the Loyalsock State Forest, Forks, PA and was sampled on June 6. Beech Lake is located in Laporte, PA and was sampled on June 11. Shumans Lake is located in Lopez, PA and was sampled on June 20. Samples from each site were strategically taken to gain knowledge of the entire body of water, including any obvious inflows and outflows. Data collected in situ included pH, dissolved oxygen, conductivity, and turbidity. Conductivity values averaged 12 µS/cm (Beech) and 14 µS/cm (Sones), but ranged from 61 to 204 µS/cm at Shumans Pond. pH at all the ponds was slightly acidic to neutral, with the lowest pH at Beech Lake (5.2 to 5.6). Alkalinity was low at all sites sampled, ranging from 1.1 to 1.6 mg/L as CaCO3 at Beech Lake to 2.4 to 9.6 mg/L as CaCO3 at Shumans Pond. Acidities were also low ranging from 2.1 to 6.0 mg/L as CaCO3 at Beech Lake to 4.6 to 13.6 mg/L as CaCO3 at Shumans Pond. Samples were analyzed for aluminum, arsenic, barium, cadmium, chromium, copper, iron, lead, manganese, nickel, and zinc using ICP-OES, with all metals except barium, iron, and manganese being below detectable limits. Both fracking and produced water from Marcellus production can be traced using conductivity, chloride, strontium, barium, and some heavy metals making pollution from Marcellus production easily detectable in these ponds should it occur – all via a sonde placed at the inflow

Assessment of Passive AMD Treatment Systems in Schuylkill County, Pennsylvania

Abandoned mine drainage (AMD) is an environmental issue of key concern in Pennsylvania. Once a rich coal mining area, Pennsylvania has been left with the consequences of abandoned or poorly regulated mines that now pollute the state’s waterways. In particular, Schuylkill County, once known for its abundance of anthracite coal, now has several AMD sites causing a change in pH and an increase in metal concentration in the water. This project analyzed five specific AMD sites which have passive treatment systems installed to mitigate the effects of the acidic drainage. The sites were Tracy Airhole, Mary D Borehole, Bell Colliery, Oneida #3, and Silver Creek. Each site is located in Schuylkill County and is part of the Northern Swatara Watershed. Tracy Airhole is west of Donaldson, Pennsylvania on SR 125 and water from this site flows into Good Spring Creek. Mary D Borehole and and Bell Colliery treatment systems are located in Mary D, Pennsylvania. Treated water from these systems flows into the Schuylkill River. The Silver Creek treatment system is in New Philadelphia, Pennsylvania and water from this system flows into Silver Creek. The project aimed to determine the water quality of these sites and assess whether the treatment systems were properly functioning. Each system was sampled once in the summer of 2017. In situ measurements using a YSI EXO2™ sonde include pH, turbidity, conductivity, dissolved oxygen, and temperature. Bulk samples were stored in 4-liter jugs in ice for transport back to the laboratory. Titrations to measure acidity and alkalinity were performed on triplicate filtered samples. Sub samples were stored for heavy metals (both unfiltered (total) and filtered (dissolved); both acidified to pH \u3c2) and simple anions and cations (filtered). Comparative results will be presented

Inorganic Geochemistry of the Susquehanna River Near Byer’S Island, Shamokin Dam (Nothumberland County) PA

In 2009, we found elevated levels of heavy metals (copper, lead, and manganese) in water samples on the eastern transect on the Susquehanna River near the middle of Byer’s Island. These were not found in either 2010 or 2011, summers with increased precip

Geochemical Baseline Study of Ten Stream Sites in the Briar Creek Watershed (Columbia County, PA) in Relation to Land Use and Geology of the Surrounding Area

Water samples were collected from 10 sites in the Briar Creek watershed on a biweekly basis from October 2011 to August 2012. In situ analyses of the samples included pH, temperature, dissolved oxygen, and conductivity. Turbidity was measured on site on

Influence of the Oneida #3 Acid Mine Drainage and Passive Limestone Treatment on System on Little Tomhicken Creek in Luzerne County PA

Discharge from the Oneida #3 abandoned coal mine drainage tunnel enters Little Tomhicken Creek near Oneida, PA. This study is part of an ongoing effort to assess the ef?cacy of a passive limestone treatment system installed in December of 2009. Samples w