Physical Sciences and Mathematics Commons^™

Contributions Of Tunneling In 8Π-6Π Electrocyclic Cascade Reactions Of Bicyclo[4.2.0]Octa-2,4-Diene Moieties, Ishika Jain, Claire Castro, William L. Karney

Featured Student Work

Six-electron electrocyclic reactions usually require relatively high temperatures; however recent research has shown that such reactions can occur at significantly lower temperatures in biosynthetic and biomimetic pathways. Pathways resulting in bicyclo[4.2.0]octa-2,4-diene moieties arise from thermally allowed 8π-6π electrocyclization cascade reactions of 1,3,5,7-octatetraenes, as in the biosynthesis of endiandric acids, elysiapyrones, and numerous other natural products. We report multidimensional tunneling calculations to explore the possible contribution of heavy-atom tunneling (e.g. by carbon) to biosynthetic pathways and biomimetic syntheses, and thus to provide a more complete picture of biochemical kinetics. M06-2X/cc-pVDZ calculations on the 8π-6π cascade cyclizations of methylated octatetraene model systems …

Substrate Specificity In Abc Transporters Using The E. Coli Methionine Import System, John H. Guardado

Featured Student Work

ATP-binding cassette (ABC) transporters use the energy of ATP to move substrates across membranes against a concentration gradient. The role of ABC transporters is crucial in several essential cellular functions and mutations in ABC transporters in humans have been linked to several conditions, including cystic fibrosis, liver disease, and diabetes. Despite their central roles in homeostasis, the mechanism of ABC transporters remains poorly understood. Our research is focused on studying an ABC importer in E. coli, as a model system, to examine the mechanism of substrate specificity and transport. The bacterial methionine import system consists of a membrane-embedded transporter, MetNI, …

Usf Jamovi Tutorial Project: Open Education Resource, Aline Hitti, Saera Khan

USF OER Faculty Grant

Jamovi is an open source free software that USF staff, faculty and student can download to carry out any statistical analyses. The current report summarizes the progress made on an Open Education Resource Grant funded project, which aimed to created Jamovi tutorials. In this report, student feedback and faculty reaction are summarized after one semester of using the tutorials created.

Finding Strong Gravitational Lenses In The Desi Decam Legacy Survey, Xiaosheng Huang, Christopher Storfer, V. Ravi, A. Pilon, M. Domingo, D. J. Schlegel, S. Bailey, A. Dey, R. R. Gupta, D. Herrera, S. Juneau, M. Landriau, D. Lang, A. Meisner, J. Moustakas, A. D. Myers, E. F. Schlafly, F. Valdes, B. A. Weaver, J. Yang, C. Yèche

Physics and Astronomy

We perform a semi-automated search for strong gravitational lensing systems in the 9000 deg2 Dark Energy Camera Legacy Survey (DECaLS), part of the Dark Energy Spectroscopic Instrument Legacy Imaging Surveys. The combination of the depth and breadth of these surveys are unparalleled at this time, making them particularly suitable for discovering new strong gravitational lensing systems. We adopt the deep residual neural network architecture developed by Lanusse et al. for the purpose of finding strong lenses in photometric surveys. We compile a training sample that consists of known lensing systems in the Legacy Surveys and the Dark Energy Survey as …

Discovering New Strong Gravitational Lenses In The Desi Legacy Imaging Surveys, Xiaosheng Huang, Christopher Storfer, A. Gu, V. Ravi, A. Pilon, W. Sheu, R. Venguswamy, S. Bankda, A. Dey, M. Landriau, D. Lang, A. Meisner, J. Moustakas, A. D. Myers, R. Sajith, E. F. Schlafly, D. J. Schlegel

Physics and Astronomy

We have conducted a search for new strong gravitational lensing systems in the Dark Energy Spectroscopic Instrument Legacy Imaging Surveys’ Data Release 8. We use deep residual neural networks, building on previous work presented in Huang et al. (2020). These surveys together cover approximately one third of the sky visible from the northern hemisphere, reaching a z-band AB magnitude of ∼ 22.5. We compile a training sample that consists of known lensing systems as well as non-lenses in the Legacy Surveys and the Dark Energy Survey. After applying our trained neural networks to the survey data, we visually inspect and …

Identifying Group Contributions In Nba Lineups With Spectral Analysis, Stephen Devlin, David Uminsky

Mathematics

We address the question of how to quantify the contributions of groups of players to team success. Our approach is based on spectral analysis, a technique from algebraic signal processing, which has several appealing features. First, our analysis decomposes the team success signal into components that are naturally understood as the contributions of player groups of a given size: individuals, pairs, triples, fours, and full five-player lineups. Secondly, the decomposition is orthogonal so that contributions of a player group can be thought of as pure: Contributions attributed to a group of three, for example, have been separated from the lower-order …

Precise Mass Determination Of Spt-Cl J2106-5844, The Most Massive Cluster At Z > 1, Jinhyub Kim, M. James Jee, Saul Perlmutter, Brian Hayden, David Rubin, Xiaosheng Huang, Greg Aldering, Jongwan Ko

Physics and Astronomy

We present a detailed high-resolution weak-lensing study of SPT-CL J2106-5844 at z = 1.132, claimed to be the most massive system discovered at z > 1 in the South Pole Telescope Sunyaev–Zel'dovich survey. Based on the deep imaging data from the Advanced Camera for Surveys and Wide Field Camera 3 on board the Hubble Space Telescope, we find that the cluster mass distribution is asymmetric, composed of a main clump and a subclump ~640 kpc west thereof. The central clump is further resolved into two smaller northwestern and southeastern substructures separated by ~150 kpc. We show that this rather complex …

The Population Densities Of Argon Metastable Levels, Nada Khogeer, Chelsy Gonzalez, Milka Nikolic

Physics and Astronomy

In this experiment, we used the optical emission spectroscopy (OES) method to obtain the main properties of low temperature Argon plasma. The experiment was sustained in powers and pressures that ranges from 30-100 W and 15-100 mTorr. We used numerical methods for the Argon kinetic model to calculate metastable levels and resonant states for the first excited states in low temperature Argon plasma. By finding the ratio of two spectral lines and finding another ratio from a different upper energy level that goes down to the same two lower energy levels, we can construct a system of two nonlinear equations. …

The Discovery Of A Gravitationally Lensed Supernova Ia At Redshift 2.22, David Rubin, Brian Hayden, Xiaosheng Huang, Greg Aldering, R Amanullah, K Barbary, K Boone, M Brodwin, S E. Deustua, S Dixon, P Eisenhardt, A S. Fruchter, A H. Gonzalez, A Goobar, R R. Gupta, I Hook, M. James Jee, A G. Kim, M Kowalski, C Lidman, E V. Linder, K Luther, J Nordin, R Pain, Saul Perlmutter, Z Raha, M Rigault, P Ruiz-Lapuente, C Saunders, C Sofiatti, A L. Spadafora, S A. Stanford, D Stern, N Suzuki, S C. Williams

Physics and Astronomy

We present the discovery and measurements of a gravitationally lensed supernova (SN) behind the galaxy cluster MOO J1014+0038. Based on multi-band Hubble Space Telescope and Very Large Telescope (VLT) photometry of the supernova, and VLT spectroscopy of the host galaxy, we find a 97.5% probability that this SN is a SN Ia, and a 2.5% chance of a CC SN. Our typing algorithm combines the shape and color of the light curve with the expected rates of each SN type in the host galaxy. With a redshift of 2.2216, this is the highest redshift SN Ia discovered with a spectroscopic …

A Network Diffusion Ranking Family That Includes The Methods Of Markov, Massey, And Colley, Stephen Devlin, Thomas Treloar

Mathematics

We present a one parameter family of ratings and rankings that includes the Markov method, as well as the methods of Colley and Massey as particular cases. The rankings are based on a natural network diffusion process that unites the methodologies above in a common framework and brings strong intuition to how and why they differ. We also explore the behavior of the ranking family using both real and simulated data.

On The Time Variation Of Dust Extinction And Gas Absorption For Type Ia Supernovae Observed Through A Nonuniform Interstellar Medium, Xiaosheng Huang, G Aldering, M. Biederman, B. Herger

Physics and Astronomy

For Type Ia supernovae (SNe Ia) observed through a nonuniform interstellar medium (ISM) in its host galaxy, we investigate whether the nonuniformity can cause observable time variations in dust extinction and in gas absorption due to the expansion of the SN photosphere with time. We show that, owing to the steep spectral index of the ISM density power spectrum, sizable density fluctuation amplitudes at the length scale of typical ISM structures () will translate to much smaller fluctuations on the scales of an SN photosphere. Therefore, the typical amplitude of time variation due to a nonuniform ISM, of absorption equivalent …

The Extinction Properties Of And Distance To The Highly Reddened Type Ia Supernova Sn 2012cu, Xiaosheng Huang, Z. Raha, G. Aldering, P. Antilogus, S. Bailey, C. Baltay, K. Barbary, D. Baugh, K. Boone, S. Bongard, C. Buton, J. Chen, N. Chotard, Y. Copin, P. Fagrelius, H. K. Fakhouri, U. Feindt, D. Fouchez, E. Gangler, B. Hayden, W. Hillebrandt, A. G. Kim, M. Kowalski, P. F. Leget, S. Lombardo, J. Nordin, R. Pain, E. Pecontal, R. Pereira, S. Perlmutter, D. Rabinowitz, M. Rigault, D. Rubin, K. Runge, C. Saunders, G. Smadja, C. Sofiatti, A. Stocker, N. Suzuki, S. Taubenberger, C. Tao, R. C. Thomas

Physics and Astronomy

Correcting Type Ia Supernova brightnesses for extinction by dust has proven to be a vexing problem. Here we study the dust foreground to the highly reddened SN 2012cu, which is projected onto a dust lane in the galaxy NGC 4772. The analysis is based on multi-epoch, spectrophotometric observations spanning from 3300–9200 Å, obtained by the Nearby Supernova Factory. Phase-matched comparison of the spectroscopically twinned SN 2012cu and SN 2011fe across 10 epochs results in the best-fit color excess of (, RMS) = (1.00, 0.03) and total-to-selective extinction ratio of (R V , RMS) = (2.95, 0.08) toward SN 2012cu …

Discussion Of "Bridging The Gap Between Theory And Practice In Basic Statistical Process Monitoring", L. A. Jones-Farmer, Nathaniel Stevens

Mathematics

No abstract provided.

Topic Supervised Non-Negative Matrix Factorization, K. Macmillan, James D. Wilson

Mathematics

Topic models have been extensively used to organize and interpret the contents of large, unstructured corpora of text documents. Although topic models often perform well on traditional training vs. test set evaluations, it is often the case that the results of a topic model do not align with human interpretation. This interpretability fallacy is largely due to the unsupervised nature of topic models, which prohibits any user guidance on the results of a model. In this paper, we introduce a semi-supervised method called topic supervised non-negative matrix factorization (TS-NMF) that enables the user to provide labeled example documents to promote …

Statistical Modeling Of The Default Mode Brain Network Reveals A Segregated Highway Structure, P. E. Stillman, James D. Wilson, M. J. Denny, B. A. Desmarais, Shankar Bhamidi, S. J. Cranmer, Zhong-Lin Lu

Mathematics

We investigate the functional organization of the Default Mode Network (DMN) – an important subnetwork within the brain associated with a wide range of higher-order cognitive functions. While past work has shown the whole-brain network of functional connectivity follows small-world organizational principles, subnetwork structure is less well understood. Current statistical tools, however, are not suited to quantifying the operating characteristics of functional networks as they often require threshold censoring of information and do not allow for inferential testing of the role that local processes play in determining network structure. Here, we develop the correlation Generalized Exponential Random Graph Model (cGERGM) …

Quantifying Similarity In Reliability Surfaces Using The Probability Of Agreement, Nathaniel Stevens, C. M. Anderson-Cook

Mathematics

When separate populations exhibit similar reliability as a function of multiple explanatory variables, combining them into a single population is tempting. This can simplify future predictions and reduce uncertainty associated with estimation. However, combining these populations may introduce bias if the underlying relationships are in fact different. The probability of agreement formally and intuitively quantifies the similarity of estimated reliability surfaces across a two-factor input space. An example from the reliability literature demonstrates the utility of the approach when deciding whether to combine two populations or to keep them as distinct. New graphical summaries provide strategies for visualizing the results.

Unboxing Cluster Heatmaps, Sophie J. Engle, S. Whalen, Alark Joshi, K. Pollard

Computer Science

Background: Cluster heatmaps are commonly used in biology and related fields to reveal hierarchical clusters in data matrices. This visualization technique has high data density and reveal clusters better than unordered heatmaps alone. However, cluster heatmaps have known issues making them both time consuming to use and prone to error. We hypothesize that visualization techniques without the rigid grid constraint of cluster heatmaps will perform better at clustering-related tasks.

Results: We developed an approach to “unbox” the heatmap values and embed them directly in the hierarchical clustering results, allowing us to use standard hierarchical visualization techniques as alternatives …

Can Community Structure Track Sea-Level Rise? Stress And Competitive Controls In Tidal Wetlands, Lisa M. Schile, John Callaway, K M. Suding, N M. Kelly

Environmental Science

Climate change impacts, such as accelerated sea-level rise, will affect stress gradients, yet impacts on competition/stress tolerance trade-offs and shifts in distributions are unclear. Ecosystems with strong stress gradients, such as estuaries, allow for space-for-time substitutions of stress factors and can give insight into future climate-related shifts in both resource and nonresource stresses. We tested the stress gradient hypothesis and examined the effect of increased inundation stress and biotic interactions on growth and survival of two congeneric wetland sedges, Schoenoplectus acutus and Schoenoplectus americanus. We simulated sea-level rise across existing marsh elevations and those not currently found to reflect …

Smoothing-Based Compressed State Kalman Filter For Joint State-Parameter Estimation: Applications In Reservoir Characterization And Co2 Storage Monitoring, Y. J. Li, Amalia Kokkinaki, E F. Darve, P K. Kitanidis

Environmental Science

The operation of most engineered hydrogeological systems relies on simulating physical processes using numerical models with uncertain parameters and initial conditions. Predictions by such uncertain models can be greatly improved by Kalman-filter techniques that sequentially assimilate monitoring data. Each assimilation constitutes a nonlinear optimization, which is solved by linearizing an objective function about the model prediction and applying a linear correction to this prediction. However, if model parameters and initial conditions are uncertain, the optimization problem becomes strongly nonlinear and a linear correction may yield unphysical results. In this paper, we investigate the utility of one-step ahead smoothing, a variant …

A Self-Calibrating Runoff And Streamflow Remote Sensing Model For Ungauged Basins Using Open-Access Earth Observation Data, A Poortinga, W Bastiaanssen, G Simons, David Saah, G Senay, M Fenn, B Bean, J Kadyszewski

Environmental Science

Due to increasing pressures on water resources, there is a need to monitor regional water resource availability in a spatially and temporally explicit manner. However, for many parts of the world, there is insufficient data to quantify stream flow or ground water infiltration rates. We present the results of a pixel-based water balance formulation to partition rainfall into evapotranspiration, surface water runoff and potential ground water infiltration. The method leverages remote sensing derived estimates of precipitation, evapotranspiration, soil moisture, Leaf Area Index, and a single F coefficient to distinguish between runoff and storage changes. The study produced significant correlations between …

A Redox-Neutral Catechol Synthesis, Q. Wu, D. Yan, Y. Chen, T. Wang, F. Xiong, W. Wei, Y. Lu, W. Sun, Jie Jack Li, J. Zhao

Chemistry Faculty Publications

Ubiquitous tyrosinase catalyses the aerobic oxidation of phenols to catechols through the binuclear copper centres. Here, inspired by the Fischer indole synthesis, we report an iridium-catalysed tyrosinase-like approach to catechols, employing an oxyacetamide-directed C–H hydroxylation on phenols. This method achieves one-step, redox-neutral synthesis of catechols with diverse substituent groups under mild conditions. Mechanistic studies confirm that the directing group (DG) oxyacetamide acts as the oxygen source. This strategy has been applied to the synthesis of different important catechols with fluorescent property and bioactivity from the corresponding phenols. Finally, our method also provides a convenient route to ¹⁸O-labelled catechols using …

A Bioinspired And Biocompatible Ortho-Sulfiliminyl Phenol Synthesis, Feng Xiong, Liang Lu, Tian-Yu Sun, Qian Wu, Dingyuan Yan, Ying Chen, Xinhao Zhang, Wei Wei, Yi Lu, Wei-Yin Sun, Jie Jack Li, Jing Zhao

Chemistry Faculty Publications

Synthetic methods inspired by Nature often offer unique advantages including mild conditions and biocompatibility with aqueous media. Inspired by an ergothioneine biosynthesis protein EgtB, a mononuclear non-haem iron enzyme capable of catalysing the C–S bond formation and sulfoxidation, herein, we discovered a mild and metal-free C–H sulfenylation/intramolecular rearrangement cascade reaction employing an internally oxidizing O–N bond as a directing group. Our strategy accommodates a variety of oxyamines with good site selectivity and intrinsic oxidative properties. Combining an O–N bond with an X–S bond generates a C–S bond and an S¼N bond rapidly. The newly discovered cascade reaction showed excellent chemoselectivity …

Early Sex Work Initiation And Condom Use Among Alcohol-Using Female Sex Workers In Mombasa, Kenya: A Cross-Sectional Analysis, A. M. Parcesepe, Kelly L'Engle, S. L. Martin, S. Green, C. Suchindran, P. Mwarogo

Nursing and Health Professions Faculty Research and Publications

Objectives Early initiation of sex work is prevalent among female sex workers (FSWs) worldwide. The objectives of this study were to investigate if early initiation of sex work was associated with: (1) consistent condom use, (2) condom negotiation self-efficacy or (3) condom use norms among alcohol-using FSWs in Mombasa, Kenya.

Methods In-person interviews were conducted with 816 FSWs in Mombasa, Kenya. Sample participants were: recruited from HIV prevention drop-in centres, 18 years or older and moderate risk drinkers. Early initiation was defined as first engaging in sex work at 17 years or younger. Logistic regression modelled outcomes as a function …

A Global Meta-Analysis Of Forest Bioenergy Greenhouse Gas Emission Accounting Studies, T Buchholz, M D. Hurteau, J Gunn, David Saah

Environmental Science

The potential greenhouse gas benefits of displacing fossil energy with biofuels are driving policy development in the absence of complete information. The potential carbon neutrality of forest biomass is a source of considerable scientific debate because of the complexity of dynamic forest ecosystems, varied feedstock types, and multiple energy production pathways. The lack of scientific consensus leaves decision makers struggling with contradicting technical advice. Analyzing previously published studies, our goal was to identify and prioritize those attributes of bioenergy greenhouse gas (GHG) emissions analysis that are most influential on length of carbon payback period. We investigated outcomes of 59 previously …

Contributions Of Organic And Inorganic Matter To Sediment Volume And Accretion In Tidal Wetlands At Steady State, J T. Morris, D C. Barber, John Callaway, R Chambers, S C. Hagen, C S. Hopkinson, B J. Johnson, P Megonigal, S C. Neubauer, T Troxler, C Wigand

Environmental Science

A mixing model derived from first principles describes the bulk density (BD) of intertidal wetland sediments as a function of loss on ignition (LOI). The model assumes that the bulk volume of sediment equates to the sum of self-packing volumes of organic and mineral components or BD = 1/[LOI/k₁ + (1-LOI)/k₂], where k₁ and k₂ are the self-packing densities of the pure organic and inorganic components, respectively. The model explained 78% of the variability in total BD when fitted to 5075 measurements drawn from 33 wetlands distributed around the conterminous United States. The …

Estimating China’S Urban Energy Demand And Co2 Emissions: A Bottom-Up Modeling Perspective, N Khanna, D Fridley, L Price, N Zhou, Stephanie Ohshita

Environmental Science

China is experiencing unprecedented urbanization with the urban share of population expected to grow to nearly 80% by 2050. Chinese urban residents consume nearly 1.6 times as much commercial energy as rural residents, and account for an even larger share of energy and carbon dioxide (CO2) emissions embodied in urban infrastructure and goods. As a result, cities can play an increasingly important role in helping China meet its future energy and CO2 intensity reduction targets. While some individual cities have conducted energy and greenhouse gas emission inventories, China lacks estimates of aggregate urban energy consumption and CO2 emissions that take …

Best Cities: Software User Guide, Stephanie Ohshita, C Fino-Chen, L Hong, N Khanna

Environmental Science

The Benchmarking and Energy-Saving Tool for Low Carbon Cities (BEST Cities) is a dynamic decision-making tool, designed to assist local policy makers and urban planners in prioritizing strategies for energy and carbon saving at the city level in China.

China’s 12^th Five-Year Plan (2011-2015) targets a reduction in carbon intensity of the economy (CO₂ emissions per unit of GDP) by 17%. In the "Low Carbon Development 2014-2015 energy saving action plan," the State Council calls for interim targets of more than 4% in 2014 and more than 3.5% in 2015. The …

Low-Carbon City Policy Databook: 72 Policy Recommendations For Chinese Cities From The Benchmarking And Energy Savings Tool For Low Carbon Cities, L Price, N Zhou, D Fridley, Stephanie Ohshita, N Khanna, Hongyou Lu, L Hong, G He, J Romankiewicz, M Hu

Environmental Science

This report is designed to help city authorities evaluate and prioritize more than 70 different policy strategies that can reduce their city’s energy use and carbon-based greenhouse gas emissions of carbon dioxide (CO2) and methane (CH4). Local government officials, researchers, and planners can utilize the report to identify policies most relevant to local circumstances and to develop a low carbon city action plan that can be implemented in phases, over a multi-year timeframe.

The policies cover nine city sectors: industry, public and commercial buildings, residential buildings, transportation, power and heat, street lighting, water & wastewater, solid waste, and urban green …

Optical Spectroscopy And Decoherence Studies Of Yb3+:Yag At 968 Nm, Thomas Böttger, C W. Thiel, R L. Cone, Y Sun, A Faraon

Physics and Astronomy

The F7/22↔F5/22 optical transitions of Yb3+ doped into Y3Al5O12 (YAG) were studied for potential quantum information and photonic signal processing applications. Absorption and fluorescence spectroscopy located the energy levels of the ground F7/22 and excited F5/22 manifolds, allowing inconsistencies between previous assignments of crystal field splittings in the literature to be resolved. These measurements reveal an unusually large splitting between the first and second levels in both the ground and excited multiplets, potentially providing for reduced sensitivity to thermally induced decoherence and spin-lattice relaxation. Spectral hole burning through two-level saturation was observed, determining the excited state lifetime to be 860 …

Altitudinal Shifts Of The Native And Introduced Flora Of California In The Context Of 20th-Century Warming, A. Wolf, Naupaka B. Zimmerman, W. R. Anderegg, P. E. Busby, J. Christensen

Biology Faculty Publications

Aim: The differential responses of plant species to climate change are of great interest and grave concern for scientists and conservationists. One underexploited resource for better understanding these changes are the records held by herbaria. Using these records to assess the responses of different groups of species across the entire flora of California, we sought to quantify the magnitude of species elevational shifts, to measure differences in shifts among functional groups and between native and introduced species, and to evaluate whether these shifts were related to the conservation of thermal niches.

Location: California.

Methods: To characterize these shifts in California, …