Random copolymer adsorption: Morita approximation compared to exact numerical simulations

We study the adsorption of ideal random lattice copolymers with correlations in the sequences on homogeneous substrates with two different methods: An analytical solution of the problem based on the constrained annealed approximation introduced by Morita in 1964 and the generating functional (GF) technique, and direct numerical simulations of lattice chains averaged over many realizations of random sequences. Both methods allow to calculate the free energy and different conformational characteristics of the adsorbed chain. The comparison of the results for random copolymers with different degree of correlations and different types of nonadsorbing monomers (neutral or repelling from the surface) shows not only qualitative but a very good quantitative agreement, especially in the cases of Bernoullian and quasi-alternating random sequences.Comment: 19 pages, 9 figure

Parameter estimation in Cox models with missing failure indicators and the OPPERA study

In a prospective cohort study, examining all participants for incidence of the condition of interest may be prohibitively expensive. For example, the "gold standard" for diagnosing temporomandibular disorder (TMD) is a physical examination by a trained clinician. In large studies, examining all participants in this manner is infeasible. Instead, it is common to use questionnaires to screen for incidence of TMD and perform the "gold standard" examination only on participants who screen positively. Unfortunately, some participants may leave the study before receiving the "gold standard" examination. Within the framework of survival analysis, this results in missing failure indicators. Motivated by the Orofacial Pain: Prospective Evaluation and Risk Assessment (OPPERA) study, a large cohort study of TMD, we propose a method for parameter estimation in survival models with missing failure indicators. We estimate the probability of being an incident case for those lacking a "gold standard" examination using logistic regression. These estimated probabilities are used to generate multiple imputations of case status for each missing examination that are combined with observed data in appropriate regression models. The variance introduced by the procedure is estimated using multiple imputation. The method can be used to estimate both regression coefficients in Cox proportional hazard models as well as incidence rates using Poisson regression. We simulate data with missing failure indicators and show that our method performs as well as or better than competing methods. Finally, we apply the proposed method to data from the OPPERA study.Comment: Version 4: 23 pages, 0 figure

On optical forces in spherical whispering gallery mode resonators

In this paper we discuss the force exerted by the field of an optical cavity on a polarizable dipole. We show that the modification of the cavity modes due to interaction with the dipole significantly alters the properties of the force. In particular, all components of the force are found to be non-conservative, and cannot, therefore, be derived from a potential energy. We also suggest a simple generalization of the standard formulas for the optical force on the dipole, which reproduces the results of calculations based on the Maxwell stress tensor.Comment: To pe published in Optics Express Focus Issue: "Collective phenomena in photonic, plasmonic and hybrid structures

Perceptions of Clickbait: A Q-Methodology Approach

Clickbait is “content whose main purpose is to attract attention and encourage visitors to click on a link to a particular web page” (“clickbait,” n.d.). The term is also generally used to refer specifically to the attention-grabbing headlines. Critics of clickbait argue that clickbait is shallow, misleading, and ubiquitous – “a new word that has become synonymous with online journalism” (Frampton, 2015). It is the subject of a small, but growing number of studies in disciplines ranging from linguistics, communications, and information sciences. Palau-Sampio (2016) analyzed linguistic strategies associated with tabloid journalism in the Spanish digital newspaper Elpais.com, concluding that there is a trend towards lower quality news reporting. In their research on Danish news sites, Blom & Hansen (2015) identified forward-referencing, specifically the use of empty pronouns to create an information gap, as a feature of clickbait headlines. Chen, Conroy & Rubin (2015) proposed that automatic identification of clickbait could draw upon three types of features: a) lexico-semantic and pragmatic linguistic patterns (e.g. unresolved pronouns, affective and suspenseful language, action words, overuse of numerals, and reverse narratives), b) incongruent image placement with a possible emotional load, and c) user reading and commenting behavior. An effort in automated identification of clickbait by Potthast, et al. (2016) achieved 79% accuracy on Twitter tweets. But debate still rages over what the word actually means (Gardiner, 2015)

Observing the End of Cold Flow Accretion using Halo Absorption Systems

We use cosmological SPH simulations to study the cool, accreted gas in two Milky Way-size galaxies through cosmic time to z=0. We find that gas from mergers and cold flow accretion results in significant amounts of cool gas in galaxy halos. This cool circum-galactic component drops precipitously once the galaxies cross the critical mass to form stable shocks, Mvir = Msh ~ 10^12 Msun. Before reaching Msh, the galaxies experience cold mode accretion (T<10^5 K) and show moderately high covering fractions in accreted gas: f_c ~ 30-50% for R10^16 cm^-2. These values are considerably lower than observed covering fractions, suggesting that outflowing gas (not included here) is important in simulating galaxies with realistic gaseous halos. Within ~500 Myr of crossing the Msh threshold, each galaxy transitions to hot mode gas accretion, and f_c drops to ~5%. The sharp transition in covering fraction is primarily a function of halo mass, not redshift. This signature should be detectable in absorption system studies that target galaxies of varying host mass, and may provide a direct observational tracer of the transition from cold flow accretion to hot mode accretion in galaxies.Comment: 6 pages, 2 figures. Minor changes to match published version (results unchanged

Low-ionization Line Emission from Starburst Galaxies: A New Probe of Galactic-Scale Outflows

We study the kinematically narrow, low-ionization line emission from a bright, starburst galaxy at z = 0.69 using slit spectroscopy obtained with Keck/LRIS. The spectrum reveals strong absorption in MgII and FeII resonance transitions with Doppler shifts of -200 to -300 km/s, indicating a cool gas outflow. Emission in MgII near and redward of systemic velocity, in concert with the observed absorption, yields a P Cygni-like line profile similar to those observed in the Ly alpha transition in Lyman Break Galaxies. Further, the MgII emission is spatially resolved, and extends significantly beyond the emission from stars and HII regions within the galaxy. Assuming the emission has a simple, symmetric surface brightness profile, we find that the gas extends to distances > ~7 kpc. We also detect several narrow FeII* fine-structure lines in emission near the systemic velocity, arising from energy levels which are radiatively excited directly from the ground state. We suggest that the MgII and FeII* emission is generated by photon scattering in the observed outflow, and emphasize that this emission is a generic prediction of outflows. These observations provide the first direct constraints on the minimum spatial extent and morphology of the wind from a distant galaxy. Estimates of these parameters are crucial for understanding the impact of outflows in driving galaxy evolution.Comment: Submitted to ApJL. 6 pages, 4 figures. Uses emulateapj forma

On the Observed W_MgII--L_[OII] Correlation in SDSS QSO Spectra

This paper investigates the effect of differential aperture loss with SDSS fibers and examines whether such selection bias would result in the observed correlation between rest-frame absorption equivalent width of MgII absorbers, Wr(2796), and mean associated [OII] luminosity, L_[OII], in SDSS QSO spectra. We demonstrate based on a Monte Carlo simulation that the observed Wr(2796) vs. L_[OII] correlation of MgII absorbers can be well-reproduced, if all galaxies found in deep surveys possess extended MgII halos and if the extent of MgII halos scales proportionally with galaxy mass as shown in previous studies. The observed correlation can be explained by a combination of (1) the known Wr(2796) vs. rho anti-correlation in galaxy and MgII absorber pairs and (2) an increasing aperture loss in the 3" diameter SDSS fiber for galaxies at larger rho. Galaxies at larger projected distances produce on average weaker MgII absorbers and weaker (or zero) L_[OII] in SDSS QSO spectra. We show that such correlation diminishes when larger fibers are adopted and is therefore not physical. While under a simple halo model the majority of MgII absorbers do not directly probe star-forming disks, they trace photo-ionized halo gas associated with galaxies. We show that because of the scaling relation between extended gas cross-section and galaxy mass, the number density evolution of the MgII absorber population as a whole provides a good measure of the cosmic star formation history.Comment: 7 pages, 5 figures, accepted for publication in MNRA

Application of metabolomics and fluxomics to increase productivity and predict product quality

Process development is routinely performed at different scales, amongst different clones, and with different optimization goals. In this work, we examine how these variables impact and relate to cell metabolism in fed-batch process, with the goal of increasing productivity and tuning product quality. Three unique CHO clones producing different IgGs were evaluated at the 250mL, 2L, and 500L scales. The impact on cell metabolism from clonal variation, reactor designs, and batch time was quantified in this work. Likewise, metabolism in turn influences final product titers and product quality profiles. To comprehensively understand this influence, over 500 extracellular metabolite time-course profiles were considered by empirical modeling, including principal component analysis (PCA) and orthogonal partial least squares (OPLS) models. Through empirical modeling, we examined the impact of metabolism on final titer. With the objective of increasing final titer, the model identified a cluster of six metabolites (out of 500+) with a shared pathway at the interface of amino acid and glycerophospholipid metabolism. The expression of these clustered metabolites correlated strongly with final product titer at multiple stages of the fed-batch run. In addition to these findings, we will share how metabolism correlated with product quality. As development batches often have different initial cell densities and growth kinetics, we also converted all supernatant metabolite expression profiles into specific consumption rates. This enabled a less biased and more straightforward comparison between batches. Likewise, a unique model comparison was enabled, one based upon metabolite concentrations (metabolomics) and one based upon metabolite fluxes (fluxomics). Both will be presented at this conference

What Determines the Incidence and Extent of MgII Absorbing Gas Around Galaxies?

We study the connections between on-going star formation, galaxy mass, and extended halo gas, in order to distinguish between starburst-driven outflows and infalling clouds that produce the majority of observed MgII absorbers at large galactic radii (>~ 10 h^{-1} kpc) and to gain insights into halo gas contents around galaxies. We present new measurements of total stellar mass (M_star), H-alpha emission line strength (EW(H-alpha)), and specific star formation rate (sSFR) for the 94 galaxies published in H.-W. Chen et al. (2010). We find that the extent of MgII absorbing gas, R_MgII, scales with M_star and sSFR, following R_MgII \propto M_star^{0.28}\times sSFR^{0.11}. The strong dependence of R_MgII on M_star is most naturally explained, if more massive galaxies possess more extended halos of cool gas and the observed MgII absorbers arise in infalling clouds which will subsequently fuel star formation in the galaxies. The additional scaling relation of R_MgII with sSFR can be understood either as accounting for extra gas supplies due to starburst outflows or as correcting for suppressed cool gas content in high-mass halos. The latter is motivated by the well-known sSFR--M_star} inverse correlation in field galaxies. Our analysis shows that a joint study of galaxies and MgII absorbers along common sightlines provides an empirical characterization of halo gaseous radius versus halo mass. A comparison study of R_MgII around red- and blue-sequence galaxies may provide the first empirical constraint for resolving the physical origin of the observed sSFR--M_star} relation in galaxies.Comment: 6 pages, 3 figures; ApJL in pres

Can k-NN imputation improve the performance of C4.5 with small software project data sets? A comparative evaluation

Missing data is a widespread problem that can affect the ability to use data to construct effective prediction systems. We investigate a common machine learning technique that can tolerate missing values, namely C4.5, to predict cost using six real world software project databases. We analyze the predictive performance after using the k-NN missing data imputation technique to see if it is better to tolerate missing data or to try to impute missing values and then apply the C4.5 algorithm. For the investigation, we simulated three missingness mechanisms, three missing data patterns, and five missing data percentages. We found that the k-NN imputation can improve the prediction accuracy of C4.5. At the same time, both C4.5 and k-NN are little affected by the missingness mechanism, but that the missing data pattern and the missing data percentage have a strong negative impact upon prediction (or imputation) accuracy particularly if the missing data percentage exceeds 40%