Topological properties defined by nets

AbstractNets are used to generalize a result of Murtinová and to define and study a class of properties related to sequential compactness

Correlation functions quantify super-resolution images and estimate apparent clustering due to over-counting

We present an analytical method to quantify clustering in super-resolution localization images of static surfaces in two dimensions. The method also describes how over-counting of labeled molecules contributes to apparent self-clustering and how the effective lateral resolution of an image can be determined. This treatment applies to clustering of proteins and lipids in membranes, where there is significant interest in using super-resolution localization techniques to probe membrane heterogeneity. When images are quantified using pair correlation functions, the magnitude of apparent clustering due to over-counting will vary inversely with the surface density of labeled molecules and does not depend on the number of times an average molecule is counted. Over-counting does not yield apparent co-clustering in double label experiments when pair cross-correlation functions are measured. We apply our analytical method to quantify the distribution of the IgE receptor (Fc{\epsilon}RI) on the plasma membranes of chemically fixed RBL-2H3 mast cells from images acquired using stochastic optical reconstruction microscopy (STORM) and scanning electron microscopy (SEM). We find that apparent clustering of labeled IgE bound to Fc{\epsilon}RI detected with both methods arises from over-counting of individual complexes. Thus our results indicate that these receptors are randomly distributed within the resolution and sensitivity limits of these experiments.Comment: 22 pages, 5 figure

DC-electric-field-induced and low-frequency electromodulation second-harmonic generation spectroscopy of Si(001)-SiO2_2 interfaces

The mechanism of DC-Electric-Field-Induced Second-Harmonic (EFISH) generation at weakly nonlinear buried Si(001)-SiO$_2$ interfaces is studied experimentally in planar Si(001)-SiO$_2$-Cr MOS structures by optical second-harmonic generation (SHG) spectroscopy with a tunable Ti:sapphire femtosecond laser. The spectral dependence of the EFISH contribution near the direct two-photon $E_1$ transition of silicon is extracted. A systematic phenomenological model of the EFISH phenomenon, including a detailed description of the space charge region (SCR) at the semiconductor-dielectric interface in accumulation, depletion, and inversion regimes, has been developed. The influence of surface quantization effects, interface states, charge traps in the oxide layer, doping concentration and oxide thickness on nonlocal screening of the DC-electric field and on breaking of inversion symmetry in the SCR is considered. The model describes EFISH generation in the SCR using a Green function formalism which takes into account all retardation and absorption effects of the fundamental and second harmonic (SH) waves, optical interference between field-dependent and field-independent contributions to the SH field and multiple reflection interference in the SiO$_2$ layer. Good agreement between the phenomenological model and our recent and new EFISH spectroscopic results is demonstrated. Finally, low-frequency electromodulated EFISH is demonstrated as a useful differential spectroscopic technique for studies of the Si-SiO$_2$ interface in silicon-based MOS structures.Comment: 31 pages, 14 figures, 1 table, figures are also available at http://kali.ilc.msu.su/articles/50/efish.ht

Biases in abundance derivations for metal-rich nebulae

Using ab-initio photoionization models of giant HII regions, we test methods for abundance determinations based on a direct measurement of the electron temperature, now possible even for moderate to high-metallicity objects. We find that, for metallicities larger than solar, the computed abundances deviate systematically from the real ones, generally by larger amounts for more metal-rich HII regions. We discuss the reasons for this, and present diagrams allowing the reader to better understand the various factors coming into play. We briefly discuss less classical methods to derive abundances in metal-rich HII regions. In particular, we comment on the interest of the oxygen and carbon recombination lines. We also show that, contrary to the case of giant HII regions, the physical conditions in bright extragalactic planetary nebulae are such that their chemical composition can be accurately derived even at high metallicities. Thus, extragalactic planetary nebulae are promising potential probes of the metallicity of the interstellar medium in the internal parts of spiral galaxies as well as in metal-rich elliptical galaxies.Comment: 15 pages, 13 figures, Accepted for publication in A&

Results from the Super Cryogenic Dark Matter Search (SuperCDMS) experiment at Soudan

We report the result of a blinded search for Weakly Interacting Massive Particles (WIMPs) using the majority of the SuperCDMS Soudan dataset. With an exposure of 1690 kg days, a single candidate event is observed, consistent with expected backgrounds. This analysis (combined with previous Ge results) sets an upper limit on the spin-independent WIMP--nucleon cross section of $1.4 \times 10^{-44}$ ($1.0 \times 10^{-44}$) cm$^2$ at 46 GeV/$c^2$. These results set the strongest limits for WIMP--germanium-nucleus interactions for masses $>$12 GeV/$c^2$

Long-distance endosome trafficking drives fungal effector production during plant infection

To cause plant disease, pathogenic fungi can secrete effector proteins into plant cells to suppress plant immunity and facilitate fungal infection. Most fungal pathogens infect plants using very long strand-like cells, called hyphae, that secrete effectors from their tips into host tissue. How fungi undergo long-distance cell signalling to regulate effector production during infection is not known. Here we show that long-distance retrograde motility of early endosomes (EEs) is necessary to trigger transcription of effector-encoding genes during plant infection by the pathogenic fungus Ustilago maydis. We demonstrate that motor-dependent retrograde EE motility is necessary for regulation of effector production and secretion during host cell invasion. We further show that retrograde signalling involves the mitogen-activated kinase Crk1 that travels on EEs and participates in control of effector production. Fungal pathogens therefore undergo long-range signalling to orchestrate host invasion

Double parton interactions in photon+3 jet events in ppbar collisions sqrt{s}=1.96 TeV

We have used a sample of photon+3 jets events collected by the D0 experiment with an integrated luminosity of about 1 fb^-1 to determine the fraction of events with double parton scattering (f_DP) in a single ppbar collision at sqrt{s}=1.96 TeV. The DP fraction and effective cross section (sigma_eff), a process-independent scale parameter related to the parton density inside the nucleon, are measured in three intervals of the second (ordered in pT) jet transverse momentum pT_jet2 within the range 15 < pT_jet2 < 30 GeV. In this range, f_DP varies between 0.23 < f_DP < 0.47, while sigma_eff has the average value sigma_eff_ave = 16.4 +- 0.3(stat) +- 2.3(syst) mb.Comment: 15 pages, 13 figure

Dependence of the ttˉt\bar{t} production cross section on the transverse momentum of the top quark

We present a measurement of the differential cross section for $t\bar{t}$ events produced in $p\bar{p}$ collisions at $\sqrt{s}=1.96$ TeV as a function of the transverse momentum ($p_T$) of the top quark. The selected events contain a high-$p_T$ lepton ($\ell$), four or more jets, and a large imbalance in $p_T$, and correspond to 1 fb${}^{-1}$ of integrated luminosity recorded with the D0 detector. Each event must have at least one candidate for a $b$ jet. Objects in the event are associated through a constrained kinematic fit to the $t\bar{t}\to WbW\bar{b} \to \ell\nu b q\bar{q}'\bar{b}$ process. Results from next-to-leading-order perturbative QCD calculations agree with the measured differential cross section. Comparisons are also provided to predictions from Monte Carlo event generators using QCD calculations at different levels of precision.Comment: 8 pages, 6 figures, 4 tables, updated to reflect the published versio