Developing new ionization strategies for characterizing structural flexibility, heterogeneity, and transformation of biopolymers

Biopolymers, such as proteins and nucleic acids, serve important functions dictated by their structural folding. Information excavated from the intricate structural arrangements of biopolymers have been proved to be vital in diagnosing diseases, unveiling disease mechanisms, and developing new drugs. A continuous effort has been put to improve the characterization techniques of these biomolecules so that more precision can be achieved in terms of detailing their structure-function relationship. Mass spectrometry (MS) is one such technique that has become very relevant for structural biology with the emergence of soft ionization techniques such as electrospray ionization (ESI). A prerequisite to the application of ESI-MS for structural investigation of biopolymers is that the tertiary or quaternary structural components need to be retained in the gas phase of MS. The subdivision of biological mass spectrometry that employs techniques and practices to preserve the native structures of biomolecules in the gas phase is now largely known as ‘native MS’. With the growing complexity of the targeted analytes, native MS promotes the inclusion of techniques that are more capable of deciphering the dynamic structural behavior of biopolymers. For example, proteins that are of intractable (very flexible) nature or that exist in multiple conformations in solution, require an MS-based approach beyond regular ESI to address these challenges. A new spray-based ionization technique namely capillary Vibrating Sharp-edge Spray Ionization (cVSSI) is demonstrated to provide improved field-free ionization capability to promote conformer preservation in the gas phase of MS, especially for the proteins possessing greater conformational flexibility in solution. Two such proteins, leptin and thioredoxin, exhibit bimodal charge state distributions (CSDs) upon the application of voltage; only a monomodal distribution is observed for field-free conditions of cVSSI. In addition, a multidevice cVSSI approach is demonstrated to achieve in-droplet hydrogen/deuterium exchange to directly probe the solution conformer heterogeneity of a well-studied protein, ubiquitin. The presence of co-existing protein solution structures under native and denaturing solution conditions have been distinguished by the isotopic distributions of deuterated ubiquitin ions. The interchange of the relative presence of the conformers within the ensembles corresponds accordingly with the degree of denaturants (methanol) added. Finally, cVSSI is demonstrated as an ionization platform to perform controlled unfolding/refolding of ubiquitin in the droplets by adding voltage sequentially. The mass spectral features are monitored carefully to detail the impacts of voltage related to structural transformations, adducts, and multimers of ubiquitin

US Buyers’ Behavior Towards Social Sustainable Certificates

Growing awareness of the fashion industry\u27s environmental footprint in terms of water and chemical use, carbon emissions, textile waste, energy usage, and water pollution has focused international attention on sustainability issues in apparel industries. To showcase their commitment to sustainability, many fashion companies turn to certifications and accreditations from third-party organizations. These certifications and accreditations not only help improve a company\u27s performance and marketability but also give them an advantage over their competitors. US textile buyers are also becoming more selective in their purchasing decisions, looking for high-quality products that are produced in a sustainable and socially responsible manner. This is driving textile manufacturers to adopt sustainable practices and to make sure they are providing the best products to their customers. Therefore, it is necessary to understand how social sustainable certificates are valued in a buyer-supplier relationship, how sustainable certificates help buyers building trust towards their suppliers, and how the authenticity of certificates influences the relationship between a buyer and their suppliers. To achieve these goals, a semi-structured interview approach was utilized to understand the U.S. fashion buyers’ perspective on social sustainable certification. The study findings revealed significant knowledge of the buyers regarding sustainable certification. The buyers talked about greenwashing, worker’s wages, child labor, fire safety, and building collapse in connection to certification. However, not all participants prioritize certifications as a factor in their decision-making process. Another finding revealed that even though the buyers are aware of what is going on in the fashion industry and they also agreed that certification does offer certain benefits, they do not practice certification requirements in real life

Spatial Distribution and Insect Associations of Frangula alnus in the Allegheny National Forest, Pennsylvania: Implications for Management

Glossy buckthorn (Frangula alnus) (Rosales: Rhamnaceae) is an invasive European shrub that threatens to displace native vegetation in roadsides and disturbed forests in North America due to its lack of natural enemies, long leaf-out periods, and its ability to survive in a multitude of soil conditions. While well understood in its native range, information regarding F. alnus in North America is lacking. Currently, the management of this invasive shrub relies on an understanding of where it can be found and thus where treatments should be applied. This research investigated the spatial distribution patterns of F. alnus and profiled the insects associated with F. alnus in the Allegheny National Forest (ANF) in Pennsylvania to explore solutions for the improved management of F. alnus. To determine the spatial distribution patterns of F. alnus, the density and presence of F. alnus were recorded in 1,412 transect sample points located on four sites. Buffer analyses were conducted to measure the relationships between proximity to unpaved forest roads (UFR) and both F. alnus density and presence. Geostatistical analyses were used to determine spatial autocorrelation between individual F. alnus samples via the creation of variograms; spatial dependency was measured via degrees of dependency. Spatial patterns were determined using spatial analyses by distance indices (SADIE). The density and abundance of F. alnus were found to be negatively associated with proximity to UFR. The maximum distance of spatial dependency between F. alnus individuals ranged from 30.9-340.8 m based on the density and 3.5-203.8 m based on the presence. We also found F. alnus to be significantly aggregated; this was expected as F. alnus is also capable of spreading by suckering. Identifying the insects associated with F. alnus could help control F. alnus. To determine the insects associated with F. alnus, arthropod samples were collected from 16 plots of F. alnus on five collection dates using an insect net and from fruit collections from F. alnus on three collection dates. The orders and morphospecies with the highest abundances were identified. The proportion of immature hemipterans relative to adults was measured as an indication of use and preference as immature stages are often less mobile and more likely to be present on plants that they prefer, particularly if the eggs were laid on that plant. Order abundance, species richness, and species diversity were measured for dependence over time. The number and identity of insects that emerged from the fruits of F. alnus and their sex ratio were recorded. The most predominant insect species found on F. alnus in the ANF was Psylla carpinicola (Hemiptera: Psyllidae) followed by Drosophila suzukii (Diptera: Drosophilidae). The collection was dominated by the orders Hemiptera (39.8%) and Diptera (22.3%). Of the hemipterans collected, 16.2 % of individuals and 36.3% of morphospecies were juveniles. Order abundance, richness, and diversity are all dependent on time. Spotted-wing drosophila D. suzukii was found to be utilizing the fruits of F. alnus for egg and larval stages. The results of this research provide recommendations for how far from the road treatments of F. alnus should be applied. Since F. alnus was found to be aggregated, we recommend precision management for increased cost efficiency and to reduce unnecessary negative effects on surrounding wildlife. This research also concludes that many insects and arachnids are associated with F. alnus. We found D. suzukii to be utilizing the fruits of F. alnus; these flies could be decreasing the germination and recruitment of F. alnus where they are found together. In the future, this research can be furthered by examining the fruit production and recruitment of F. alnus existing further into the forest to determine whether they pose a threat and require treatment. We also suggest a more in-depth investigation regarding the nature of the relationships between the insects found to be most prevalent on F. alnus. Lastly, the effects of D. suzukii on F. alnus may be further investigated to determine the degree to which D. suzukii mitigates F. alnus

Computerized Trajectory Analysis for Firearms Examiners

Trajectory determination is a very important part of understanding and reconstructing a shooting scene. Conditions for the scene vary for each crime committed, but the evidence left at the scene required to make a reconstruction remains similar. The job of the examiner is to collect the evidence left at the scene and use that evidence to establish what may have happened during the commission of the crime. There is also important information that an examiner may not be privy to, e.g., the firearm and cartridge used. In this case, the evidence that is present, and other gathered information can be used to estimate certain required conditions such as muzzle velocity. There are many external elements that can affect the trajectory of a bullet, such as air resistance, lift, and wind. There are also characteristics of the bullet such as weight, caliber, and shape that can affect the trajectory. At the scene, most often an examiner will collect a bullet and gather impact angle information from a bullet hole to help with trajectory determination. This project examined the determination of possible trajectories based on examiner measurements at a ‘scene’. A Glock 19 (G19) pistol was used to fire into plywood squares at various angle combinations. This helped to simulate different target placements found at a shooting scene. A combination of four different vertical angles and three different azimuthal angles were for the shooting of the twenty-four boards. Factors such as ricochet and damage resulted in measurements being performed on sixteen boards. Eighteen participants repeated the measuring process three times. All the measurements were analyzed to determine reproducibility. These measurements were used to reconstruct the trajectories. The effect of error in angular measurement on trajectory reconstruction was evaluated. The results from this study demonstrated that the largest error was associated with the measurement of the azimuthal angles. This is likely due to method of measurement and the skill of the participant. In all but one board the quasi-ground truth measurements were within the 95% confidence ellipse of the data. The study also demonstrated that small changes in the angle measurements can result in a large variations in potential shooter positions as determined by the trajectory calculation

Synthesis of Quasi-Freestanding Graphene Films Using Radical Species Formed in Cold Plasmas

For over a decade, the Stinespring laboratory has investigated scalable, plasma assisted synthesis (PAS) methods for the growth of graphene films on silicon carbide (SiC). These typically utilized CF4-based inductively coupled plasma (ICP) with reactive ion etching (RIE) to selectively etch silicon from the SiC lattice. This yielded a halogenated carbon-rich surface layer which was then annealed to produce the graphene layers. The thickness of the films was controlled by the plasma parameters, and overall, the process was readily scalable to the diameter of the SiC wafer. The PAS process reproducibly yielded two- to three-layer thick graphene films that were highly tethered to the underlying SiC substrate via an intermediate buffer layer. The buffer layer was compositionally similar to graphene. However, a significant number of graphene carbons were covalently bound to silicon atoms in the underlying substrate. This tethering lead to mixing of the film and substrate energy bands which degraded many of graphene’s most desirable electrical properties. The research described in this dissertation was aimed at improving graphene quality by reducing the extent of tethering using a fundamentally different plasma etching mechanism while maintaining scalability. In the ICP-RIE process, the etchant species include F and CFx (x = 1-3) radicals and their corresponding positive ions. These radicals are classified as “cold plasma species” in the sense that they are nominally in thermal equilibrium with the substrate and walls of the system. In contrast, the electrons exist at extremely high temperature (energy), and the ionic species are accelerated to energies on the order of several hundred electron volts by the plasma bias voltage that exists between the plasma and substrate. As a result, the ionic species create a directional, high rate etch that is dominated by physical etching characterized by energy and momentum transfer. In contrast, the neutral radicals chemically etch the surface at a much lower rate. In this work, the effects of physical etching due to high energy ions were eliminated by shielding the SiC substrate using a mask (e.g., quartz) supported by silicon posts. In this way, a microplasma consisting of chemically reactive cold plasma species was created in the small space between the substrate surface and the backside of the quartz mask. This process, referred to here as microplasma assisted synthesis (MPAS), was used to produce graphene films. A parametric investigation was conducted to determine the influence of MPAS operating parameters on graphene quality. The key parameters investigated included ICP power, RIE power, etch time, various mask materials, microreactor height, substrate cooling, initial surface morphology and SiC polytype. The resulting graphene films were characterized by x-ray photoelectron spectroscopy (XPS), Raman spectroscopy, and atomic force microscopy (AFM). Following optimization of the MPAS process, some tethering of the graphene films remained. However, films produced by MPAS consistently exhibited significantly less tethering than those produced using the PAS process. Moreover, both XPS and Raman spectroscopy indicated that these films were quasi-free standing, and, in some cases, they approached free standing graphene. From a wide view, the results of these studies demonstrate the potential of MPAS as a technique for realizing the controlled synthesis of high-quality, lightly tethered mono-, and few-layer graphene films directly on an insulating substrate. On a more fundamental level, the results of these studies provide insight into the surface chemistry of radical species

Looking Inward, Looking Back: John le Carré and the Spy Narrative after the Cold War

The genre of spy fiction confronts a paradigm-shifting event in the 1990s with the end of the Cold War. Despite critical speculation that the genre had outlived its usefulness, spy fiction writers navigate this period of transition, and the genre remains broadly popular with the reading public. This study examines how the work of Britain’s foremost espionage writer, John le Carré, navigates the changing geopolitical landscape of the late twentieth and early twenty-first century. In mapping this terrain, one sees two distinct impulses emerge: a tendency to look inward and a tendency to look back. To look inward, the novels The Night Manager and The Constant Gardener reconfigure their conflicts to center on an amateur spy as he battles domestic antagonists who most often take the form of corrupt businessmen and government officials. Analyses of these novels will employ new economic criticism to demonstrate how, in casting neoliberal forces as the villains, the novels attempt to critique and push back against the ideological hegemony of neoliberalism. The impulse to look back involves the trend of revisiting le Carré’s Cold War novels as film and television adaptations reconceptualized for twenty-first century audiences. The television adaptation of The Little Drummer Girl and the film adaptation of Tinker Tailor Soldier Spy both engage with their original contexts and speak to the contemporary moment. Exploring the relationship between novel and adaptation establishes the ways in which an adaptation like The Little Drummer Girl can update the novel’s gender politics and geopolitical alignment in ways that enlighten both the present and the past. Likewise, putting Tinker Tailor Soldier Spy in conversation with its Cold War context provides the audience with a clear warning about the dangers of nostalgizing the complexities of the Cold War. In exploring these two different areas of le Carré’s work, this study demonstrates the flexibility of the spy narrative and its continued relevance as a genre that can speak on the relevant issues of its time

Sense and Sensitivity: Spatial Structure of conspecific signals during social interaction

Organisms rely on sensory systems to gather information about their environment. Localizing the source of a signal is key in guiding the behavior of the animal successfully. Localization mechanisms must cope with the challenges of representing the spatial information of weak, noisy signals. In this dissertation, I investigate the spatial dynamics of natural stimuli and explore how the electrosensory system of weakly electric fish encodes these realistic spatial signals. To do so In Chapter 2, I develop a model that examines the strength of the signal as it reaches the sensory array and simulates the responses of the receptors. The results demonstrate that beyond distances of 20 cm, the signal strength is only a fraction of the self-generated signal, often measuring less than a few percent. Chapter 2 also focuses on modeling a heterogeneous population of receptors to gain insights into the encoding of the spatial signal perceived by the fish. The findings reveal a significant decrease in signal detection beyond 40 cm, with a corresponding decrease in localization accuracy at 30 cm. Additionally, I investigate the impact of receptor density differences between the front and back on both signal detection and resolution accuracy. In Chapter 3, I analyze distinct movement patterns observed during agonistic encounters and their correlation with the estimated range of receptor sensitivity. Furthermore, I uncover that these agonistic interactions follow a classical pattern of cumulative assessment of competitors\u27 abilities. The outcome of this research is a comprehensive understanding of the spatial dynamics of social interactions and how this information is captured by the sensory system. Moreover, the research contributed to the development of a range of tools and models that will play crucial roles in future investigations of sensory processing within this system

Forecasting and Optimizing Sensitivity to Low-Frequency Gravitational Waves

Pulsars are among the most exotic objects in our Universe. These rapidlyspinning, high magnetic field neutron stars can be used for a wide range ofscientific studies: from the makeup of their own extremely dense and poorlyunderstood interior to using their extremely regular signals to detect gravita-tional waves (GWs). Pulsar timing continues to expand to broader communi-ties, with larger and more sensitive radio telescopes planned and partnershipsbetween pulsar timing arrays (PTAs) that span the entire globe. A realm ofnew physics with the detection of a background hum of gravitational wavesfrom black holes merging from across the Universe is close at hand. This istruly the age of pulsar timing for low-frequency GW astrophysics.With this work, we seek to expand the current techniques of pulsar timingto the bright future which makes use of Bayesian statistical techniques by moretightly integrating pulsar timing model fits into the current PTA GW analysismethodology. We examine four binary millisecond pulsars, PSRs J1640+2224,J2043+1711, J1600–3053, and J0740+6620, using our generalized Bayesianpulsar timing methods and find consistency with and often improvement uponpublished parameter constraints estimated by general least-squares timingmethods. Our new pulsar masses constraints (medians and 68% confidenceintervals) for our fully general Bayesian timing models are mp = 1.6±1 M⊙ forJ2043+1711 and mp = 2.3+0.9−0.7 M⊙ for J1600–3053, both using the NANOGrav12.5-yr data release, and mp = 2.06 ± 6 M⊙ for J0740+6620 using the datafrom Fonseca et al. (2021).We then assess the sensitivity of current and future GW detectors to in-piralling binary black holes (BBHs). We developed the tool, gwent, for cal-culating detector sensitivities in the three primary GW detector regimes ofground-based, space-based, and PTA GW observatories. We calculate realis-tic signal-to-noise ratios using multi-parameter GW source models and findregions of overlap between ground and space-based observatories as well asspace-based detectors and PTAs for non-spinning, equal mass ratio binaries.We finally use realistic simulated PTA data to assess the detectablil-ity of multiple GW backgrounds (GWBs) simultaneously. We simulate twoGWBs, one from supermassive binary black holes (SMBBHs) with spectrumof γ = 13/3, and a GWB from primordial gravitational waves (PGWs) with aspectrum of γ = 5 that has half the energy density at a frequency of f = 1/yras the SMBBH GWB. We find that the weaker, steeper PGW GWB showsevidence for separability from the stronger, shallower SMBBH GWB after 17years of data. With 20 years of data, we can constrain the injected underlyingPGW GWB spectral index and amplitude to 64% and 110%, respectively. Weuse our findings and methods to outline a basic protocol to search for multiplebackgrounds in future PTA datasets

Adventures in Flute Playing: A Literature Survey and Anticipated Beginning Flute Method

This Literature Survey will investigate 10 method books used by beginning flute students, aged 6-13, in the United States. In this survey, books will be analyzed to identify which musical concepts are covered and their overall methodical approach. Comprehensive graphs are offered in the Appendix to provide readers brief contextual information on the books analyzed. The results from this survey have influenced the creation of my beginning flute method, Adventures in Flute Playing, which incorporates exercises that are less commonly found in the method books being used today. Adventures in Flute Playing will consist of a series of online videos with a guidebook of supplemental exercises available for purchase via hard copy or PDF digital download. The Adventures in Flute Playing guidebook will be available for purchase for flute teachers, parents, and music vendors. QR Codes are placed throughout the guidebook to provide users easy access to video demonstrations and practice videos. The intended audience for Adventures in Flute Playing is beginning grade school and middle school students; however, beginners of all levels could find this method helpful