Efficient Implementation of Elastohydrodynamics via Integral Operators

The dynamics of geometrically non-linear flexible filaments play an important role in a host of biological processes, from flagella-driven cell transport to the polymeric structure of complex fluids. Such problems have historically been computationally expensive due to numerical stiffness associated with the inextensibility constraint, as well as the often non-trivial boundary conditions on the governing high-order PDEs. Formulating the problem for the evolving shape of a filament via an integral equation in the tangent angle has recently been found to greatly alleviate this numerical stiffness. The contribution of the present manuscript is to enable the simulation of non-local interactions of multiple filaments in a computationally efficient manner using the method of regularized stokeslets within this framework. The proposed method is benchmarked against a non-local bead and link model, and recent code utilizing a local drag velocity law. Systems of multiple filaments (1) in a background fluid flow, (2) under a constant body force, and (3) undergoing active self-motility are modeled efficiently. Buckling instabilities are analyzed by examining the evolving filament curvature, as well as by coarse-graining the body frame tangent angles using a Chebyshev approximation for various choices of the relevant non-dimensional parameters. From these experiments, insight is gained into how filament-filament interactions can promote buckling, and further reveal the complex fluid dynamics resulting from arrays of these interacting fibers. By examining active moment-driven filaments, we investigate the speed of worm- and sperm-like swimmers for different governing parameters. The MATLAB(R) implementation is made available as an open-source library, enabling flexible extension for alternate discretizations and different surrounding flows.Comment: 37 pages, 17 figure

Digital Single-Cell Analysis of Plant Organ Development Using 3DCellAtlas

Diverse molecular networks underlying plant growth and development are rapidly being uncovered. Integrating these data into the spatial and temporal context of dynamic organ growth remains a technical challenge. We developed 3DCellAtlas, an integrative computational pipeline that semiautomatically identifies cell types and quantifies both 3D cellular anisotropy and reporter abundance at single-cell resolution across whole plant organs. Cell identification is no less than 97.8% accurate and does not require transgenic lineage markers or reference atlases. Cell positions within organs are defined using an internal indexing system generating cellular level organ atlases where data from multiple samples can be integrated. Using this approach, we quantified the organ-wide cell-type-specific 3D cellular anisotropy driving Arabidopsis thaliana hypocotyl elongation. The impact ethylene has on hypocotyl 3D cell anisotropy identified the preferential growth of endodermis in response to this hormone. The spatiotemporal dynamics of the endogenous DELLA protein RGA, expansin gene EXPA3, and cell expansion was quantified within distinct cell types of Arabidopsis roots. A significant regulatory relationship between RGA, EXPA3, and growth was present in the epidermis and endodermis. The use of single-cell analyses of plant development enables the dynamics of diverse regulatory networks to be integrated with 3D organ growth.</p

High-resolution mass models of dwarf galaxies from LITTLE THINGS

We present high-resolution rotation curves and mass models of 26 dwarf galaxies from LITTLE THINGS. LITTLE THINGS is a high-resolution Very Large Array HI survey for nearby dwarf galaxies in the local volume within 11 Mpc. The rotation curves of the sample galaxies derived in a homogeneous and consistent manner are combined with Spitzer archival 3.6 micron and ancillary optical U, B, and V images to construct mass models of the galaxies. We decompose the rotation curves in terms of the dynamical contributions by baryons and dark matter halos, and compare the latter with those of dwarf galaxies from THINGS as well as Lambda CDM SPH simulations in which the effect of baryonic feedback processes is included. Being generally consistent with THINGS and simulated dwarf galaxies, most of the LITTLE THINGS sample galaxies show a linear increase of the rotation curve in their inner regions, which gives shallower logarithmic inner slopes alpha of their dark matter density profiles. The mean value of the slopes of the 26 LITTLE THINGS dwarf galaxies is alpha =-0.32 +/- 0.24 which is in accordance with the previous results found for low surface brightness galaxies (alpha = -0.2 +/- 0.2) as well as the seven THINGS dwarf galaxies (alpha =-0.29 +/- 0.07). However, this significantly deviates from the cusp-like dark matter distribution predicted by dark-matter-only Lambda CDM simulations. Instead our results are more in line with the shallower slopes found in the Lambda CDM SPH simulations of dwarf galaxies in which the effect of baryonic feedback processes is included. In addition, we discuss the central dark matter distribution of DDO 210 whose stellar mass is relatively low in our sample to examine the scenario of inefficient supernova feedback in low mass dwarf galaxies predicted from recent Lambda SPH simulations of dwarf galaxies where central cusps still remain.Peer reviewe

The Circumgalactic Medium in Massive Halos

This chapter presents a review of the current state of knowledge on the cool (T ~ 1e4 K) halo gas content around massive galaxies at z ~ 0.2-2. Over the last decade, significant progress has been made in characterizing the cool circumgalactic gas in massive halos of Mh ~ 1e12-1e14 Msun at intermediate redshifts using absorption spectroscopy. Systematic studies of halo gas around massive galaxies beyond the nearby universe are made possible by large spectroscopic samples of galaxies and quasars in public archives. In addition to accurate and precise constraints for the incidence of cool gas in massive halos, detailed characterizations of gas kinematics and chemical compositions around massive quiescent galaxies at z ~ 0.5 have also been obtained. Combining all available measurements shows that infalling clouds from external sources are likely the primary source of cool gas detected at d >~ 100 kpc from massive quiescent galaxies. The origin of the gas closer in is currently less certain, but SNe Ia driven winds appear to contribute significantly to cool gas found at d < 100 kpc. In contrast, cool gas observed at d <~ 200 kpc from luminous quasars appears to be intimately connected to quasar activities on parsec scales. The observed strong correlation between cool gas covering fraction in quasar host halos and quasar bolometric luminosity remains a puzzle. Combining absorption-line studies with spatially-resolved emission measurements of both gas and galaxies is the necessary next step to address remaining questions.Comment: 29 pages, 7 figures, invited review to appear in "Gas Accretion onto Galaxies", Astrophysics and Space Science Library, eds. A. Fox & R. Dave, to be published by Springe

Irreducible tensor-form of the relativistic corrections to the M1 transition operator

The relativistic corrections to the magnetic dipole moment operator in the Pauli approximation were derived originally by Drake (Phys. Rev. A 3(1971)908). In the present paper, we derive their irreducible tensor-operator form to be used in atomic structure codes adopting the Fano-Racah-Wigner algebra for calculating its matrix elements.Comment: 26 page

Identification and thermochemical analysis of high-lignin feedstocks for biofuel and biochemical production

Background - Lignin is a highly abundant biopolymer synthesized by plants as a complex component of plant secondary cell walls. Efforts to utilize lignin-based bioproducts are needed. Results - Herein we identify and characterize the composition and pyrolytic deconstruction characteristics of high-lignin feedstocks. Feedstocks displaying the highest levels of lignin were identified as drupe endocarp biomass arising as agricultural waste from horticultural crops. By performing pyrolysis coupled to gas chromatography-mass spectrometry, we characterized lignin-derived deconstruction products from endocarp biomass and compared these with switchgrass. By comparing individual pyrolytic products, we document higher amounts of acetic acid, 1-hydroxy-2-propanone, acetone and furfural in switchgrass compared to endocarp tissue, which is consistent with high holocellulose relative to lignin. By contrast, greater yields of lignin-based pyrolytic products such as phenol, 2-methoxyphenol, 2-methylphenol, 2-methoxy-4-methylphenol and 4-ethyl-2-methoxyphenol arising from drupe endocarp tissue are documented. Conclusions - Differences in product yield, thermal decomposition rates and molecular species distribution among the feedstocks illustrate the potential of high-lignin endocarp feedstocks to generate valuable chemicals by thermochemical deconstruction

Crop pests and predators exhibit inconsistent responses to surrounding landscape composition

The idea that noncrop habitat enhances pest control and represents a win–win opportunity to conserve biodiversity and bolster yields has emerged as an agroecological paradigm. However, while noncrop habitat in landscapes surrounding farms sometimes benefits pest predators, natural enemy responses remain heterogeneous across studies and effects on pests are inconclusive. The observed heterogeneity in species responses to noncrop habitat may be biological in origin or could result from variation in how habitat and biocontrol are measured. Here, we use a pest-control database encompassing 132 studies and 6,759 sites worldwide to model natural enemy and pest abundances, predation rates, and crop damage as a function of landscape composition. Our results showed that although landscape composition explained significant variation within studies, pest and enemy abundances, predation rates, crop damage, and yields each exhibited different responses across studies, sometimes increasing and sometimes decreasing in landscapes with more noncrop habitat but overall showing no consistent trend. Thus, models that used landscape-composition variables to predict pest-control dynamics demonstrated little potential to explain variation across studies, though prediction did improve when comparing studies with similar crop and landscape features. Overall, our work shows that surrounding noncrop habitat does not consistently improve pest management, meaning habitat conservation may bolster production in some systems and depress yields in others. Future efforts to develop tools that inform farmers when habitat conservation truly represents a win–win would benefit from increased understanding of how landscape effects are modulated by local farm management and the biology of pests and their enemies

Antiinflammatory Therapy with Canakinumab for Atherosclerotic Disease

Background: Experimental and clinical data suggest that reducing inflammation without affecting lipid levels may reduce the risk of cardiovascular disease. Yet, the inflammatory hypothesis of atherothrombosis has remained unproved. Methods: We conducted a randomized, double-blind trial of canakinumab, a therapeutic monoclonal antibody targeting interleukin-1β, involving 10,061 patients with previous myocardial infarction and a high-sensitivity C-reactive protein level of 2 mg or more per liter. The trial compared three doses of canakinumab (50 mg, 150 mg, and 300 mg, administered subcutaneously every 3 months) with placebo. The primary efficacy end point was nonfatal myocardial infarction, nonfatal stroke, or cardiovascular death. RESULTS: At 48 months, the median reduction from baseline in the high-sensitivity C-reactive protein level was 26 percentage points greater in the group that received the 50-mg dose of canakinumab, 37 percentage points greater in the 150-mg group, and 41 percentage points greater in the 300-mg group than in the placebo group. Canakinumab did not reduce lipid levels from baseline. At a median follow-up of 3.7 years, the incidence rate for the primary end point was 4.50 events per 100 person-years in the placebo group, 4.11 events per 100 person-years in the 50-mg group, 3.86 events per 100 person-years in the 150-mg group, and 3.90 events per 100 person-years in the 300-mg group. The hazard ratios as compared with placebo were as follows: in the 50-mg group, 0.93 (95% confidence interval [CI], 0.80 to 1.07; P = 0.30); in the 150-mg group, 0.85 (95% CI, 0.74 to 0.98; P = 0.021); and in the 300-mg group, 0.86 (95% CI, 0.75 to 0.99; P = 0.031). The 150-mg dose, but not the other doses, met the prespecified multiplicity-adjusted threshold for statistical significance for the primary end point and the secondary end point that additionally included hospitalization for unstable angina that led to urgent revascularization (hazard ratio vs. placebo, 0.83; 95% CI, 0.73 to 0.95; P = 0.005). Canakinumab was associated with a higher incidence of fatal infection than was placebo. There was no significant difference in all-cause mortality (hazard ratio for all canakinumab doses vs. placebo, 0.94; 95% CI, 0.83 to 1.06; P = 0.31). Conclusions: Antiinflammatory therapy targeting the interleukin-1β innate immunity pathway with canakinumab at a dose of 150 mg every 3 months led to a significantly lower rate of recurrent cardiovascular events than placebo, independent of lipid-level lowering. (Funded by Novartis; CANTOS ClinicalTrials.gov number, NCT01327846.