P-Cygni Type Lya from Starburst Galaxies

P-Cygni type Lya profiles exhibited in nearly half of starburst galaxies, both nearby and high-z, are believed to be formed by an expanding supershell surrounding a star-forming region. We apply the Monte Carlo code which was developed previously for static and plane-parallel medium to calculate the Lya line transfer in a supershell of neutral hydrogen which are expanding radially in a spherical bulk flow. We consider typical cases that the supershell has the Lya line-centre optical depth of $\tau_0=10^5-10^7$, a radial expansion velocity of $V_exp = 300 km/s, and the turbulence of b=40 km/s. We find that there appear a few emission peaks at the frequencies corresponding to (2N-1) V_exp, where the order of back scatterings N > 1. As V_exp -> b, the emergent profiles become similar to those for the static medium and the peaks are less prominent. We also investigate the effects of column density of the supershell on the emergent Lya profiles. We find that the number and the flux ratios of emission peaks are determined by interplay of$\tau_0$ and V_exp of the supershell. We discuss the effects of dust extinction and the implication of our works in relation to recent spectroscopic observations of starburst galaxies.Comment: 15 pages, 6 figures, submitted to MNRA

Improving User Involvement Through Live Collaborative Creation

Creating an artifact - such as writing a book, developing software, or performing a piece of music - is often limited to those with domain-specific experience or training. As a consequence, effectively involving non-expert end users in such creative processes is challenging. This work explores how computational systems can facilitate collaboration, communication, and participation in the context of involving users in the process of creating artifacts while mitigating the challenges inherent to such processes. In particular, the interactive systems presented in this work support live collaborative creation, in which artifact users collaboratively participate in the artifact creation process with creators in real time. In the systems that I have created, I explored liveness, the extent to which the process of creating artifacts and the state of the artifacts are immediately and continuously perceptible, for applications such as programming, writing, music performance, and UI design. Liveness helps preserve natural expressivity, supports real-time communication, and facilitates participation in the creative process. Live collaboration is beneficial for users and creators alike: making the process of creation visible encourages users to engage in the process and better understand the final artifact. Additionally, creators can receive immediate feedback in a continuous, closed loop with users. Through these interactive systems, non-expert participants help create such artifacts as GUI prototypes, software, and musical performances. This dissertation explores three topics: (1) the challenges inherent to collaborative creation in live settings, and computational tools that address them; (2) methods for reducing the barriers of entry to live collaboration; and (3) approaches to preserving liveness in the creative process, affording creators more expressivity in making artifacts and affording users access to information traditionally only available in real-time processes. In this work, I showed that enabling collaborative, expressive, and live interactions in computational systems allow the broader population to take part in various creative practices.PHDComputer Science & EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/145810/1/snaglee_1.pd

Effects of Surface Topography on Bacterial Biofilm Formation

Biofilms are multicellular structures with bacterial cells attached to a surface and embedded in an extracellular matrix. With high-level resistance to antimicrobial agents, biofilms are the cause of chronic infections associated with implanted medical devices such as breast implants, orthopedic devices, pace markers, and many others. Besides the prevalence, biofilm infections are associated with high mortality, presenting an urgent need for more effective controls. Several strategies such as coating with antimicrobial agents and changing chemical, physical, and biological properties of biomaterials have been attempted, but bacteria have remarkable capabilities to overcome unfavorable conditions over time and long-term biofilm control remains challenging. In addition, most approaches are based on empirical experiments rather than rational designs, limiting their effects, especially in vivo. In this study, we engineered surface topography in two ways (static and dynamic) to better understand and control bacterial biofilm formation. For the static surface topography, a high-throughput approach to study bacterial attachment on PDMS surfaces with different textures was developed. By testing bacterial adhesion to samples with square-shaped recessive patterns with varying size and inter-pattern distance, surface features that promote biofilm formation were identified. E. coli attachment did not exhibit a monotonic, linear relationship with surface area, but depended on the 3D topography. For dynamic surface topography, we used shape memory polymers (SMPs) to obtain on-demand dynamic changes in substratum topography. Our results show that shape recovery of tert-butyl acrylate (tBA) based one-way SMP caused 99.9% detachment of 48 h Pseudomonas aeruginosa PAO1 biofilms. Interestingly, P. aeruginosa PAO1 biofilm cells detached by shape recovery showed 2,479 times higher antibiotic susceptibility compared to the original biofilm cells. The released biofilm cells also presented 4.1 times higher expression of the gene rrnB, encoding ribosomal RNA, and 11.8 times more production of adenosine triphosphate (ATP) than the control biofilm cells. To further develop this technology for long-term biofilm control, we synthesized reversible SMP with different molecular weights of poly(ɛ-caprolactone) diisocyanatoethyl dimethacrylate (PCLDIMA), with 25 wt.% of butyl acrylate (BA) as a linker, and 1 wt.% of benzoyl peroxide (BPO) as a thermal initiator. Among various combinations of molecular weight, 2:1 wt. ratio mixture of 15,000 g/mol PCLDIMA and 2,000 g/mol PCLDIMA showed a transition temperature of 36.7°C. The created rSMP has repeatable and reversible shape recovery for more than 3 cycles. With 18% stretch, 61.0±6.6% of 48 h P. aeruginosa PAO1 biofilm cells were removed in each shape recovery cycle on average, with a total of 94.3±1.0% biofilm removal after three consecutive shape recovery cycles. In summary, the results of this study demonstrated that surface topography has potent effects on bacterial adhesion and biofilm formation. We believe that these results not only provide important information for understanding the risk of medical devices but also helps the design of control methods for preventing chronic infections associated with implanted medical devices

Evolving Bacterial Envelopes and Plasticity of TLR2-Dependent Responses: Basic Research and Translational Opportunities.

Innate immune mechanisms that follow early recognition of microbes influence the nature and magnitude of subsequent adaptive immune responses. Early detection of microbes depends on pattern recognition receptors that sense pathogen-associated molecular patterns or microbial-associated molecular patterns (PAMPS or MAMPs, respectively). The bacterial envelope contains MAMPs that include membrane proteins, lipopeptides, glycopolymers, and other pro-inflammatory molecules. Bacteria are selected by environmental pressures resulting in quantitative or qualitative changes in their envelope structures that often promote evasion of host immune responses and therefore, infection. However, recent studies have shown that slight, adaptive changes in MAMPs on the bacterial cell wall may result in their ability to induce the secretion not only of pro-inflammatory cytokines but also of anti-inflammatory cytokines. This effect can fine-tune the subsequent response to microbes expressing these MAMPs and lead to the establishment of a commensal state within the host rather than infectious disease. In this review, we will examine the plasticity of Toll-like receptor (TLR) 2 signaling as evidence of evolving MAMPs, using the better-characterized TLR4 as a template. We will review the role of differential dimerization of TLR2 and the arrangement of signaling complexes and co-receptors in determining the capacity of the host to recognize an array of TLR2 ligands and generate different immune responses to these ligands. Last, we will assess briefly how this plasticity may expand the array of interactions between microbes and immune systems beyond the traditional disease-causing paradigm

Fourier transform ion cyclotron resonance study of multiply charged aggregates of small singly charged peptides formed by electrospray ionization

AbstractAggregates of singly protonated peptides formed with a nanoelectrospray ion source have been observed in the gas phase using Fourier transform ion cyclotron resonance (FT-ICR). Employment of “soft” ion sampling conditions in the source, which were developed previously to generate water clusters of biomolecules, provides significant yields of aggregates of singly protonated GGDPG ([2GGDPG + 2H]2+), GGEPG ([2GGEPG + 2H]2+), and VEPIPY (2VEPIPY + 2H]2+). With peptide mixtures, heteroaggregates, e.g., [GGDPG + GGEPG + 2H]2+ have also been observed along with the homoaggregates. These weakly bound noncovalent complexes undergo facile exothermic dissociation into the corresponding singly protonated monomer species with normal operation of the electrospray ion source. For example, the aggregates were not observed in FT-ICR experiments utilizing a conventional electrospray ionization (ESI) or fast atom bombardment source or with a quadrupolar ion trap mass spectrometer equipped with a conventional ESI source. The formation and metastability of these aggregates are dependent on highly specific intermolecular hydrogen bonding between the monomers. The amino acid sequence (DPG) of GGDPG mimics the well-known β reverse turn of proteins and semiempirical calculations show that it provides excellent hydrogen bonding sites for a protonated N-terminus amino group. Support for this conjecture is provided by the failure to observe aggregate formation of singly protonated peptides with several larger peptides, including hexaglycine and hexaalanine

Hooking up Web Audio to WebGL Typography

Presented at the 2nd Web Audio Conference (WAC), April 4-6, 2016, Atlanta, Georgia.This presentation was presented as part of a poster/demo session on April 5, 2016. Timestamp: 09:41 - 10:31.This demo introduces programmable text rendering that enables temporal typography in web browsers. Textual interaction is seen not only as a dynamic but interactive process facilitating both scripted and live musical expression in various contexts such as audio-visual performance using keyboards and live coding visualization. We transform plain text into a highly audiovisual medium and a musical interface which is visually expressive by transforming textual properties using real-time web audio signal. Technical realization of the concept uses Web Audio API, WebGL and GLSL shaders. We show a number of examples that illustrate instances of the concept in various scenarios ranging from simple textual visualization, live coding environments and interactive writing platform