Statistical Mechanics of finite arrays of coupled bistable elements

We discuss the equilibrium of a single collective variable characterizing a finite set of coupled, noisy, bistable systems as the noise strength, the size and the coupling parameter are varied. We identify distinct regions in parameter space. The results obtained in prior works in the asymptotic infinite size limit are significantly different from the finite size results. A procedure to construct approximate 1-dimensional Langevin equation is adopted. This equation provides a useful tool to understand the collective behavior even in the presence of an external driving force

Extended Kramers-Moyal analysis applied to optical trapping

The Kramers-Moyal analysis is a well established approach to analyze stochastic time series from complex systems. If the sampling interval of a measured time series is too low, systematic errors occur in the analysis results. These errors are labeled as finite time effects in the literature. In the present article, we present some new insights about these effects and discuss the limitations of a previously published method to estimate Kramers-Moyal coefficients at the presence of finite time effects. To increase the reliability of this method and to avoid misinterpretations, we extend it by the computation of error estimates for estimated parameters using a Monte Carlo error propagation technique. Finally, the extended method is applied to a data set of an optical trapping experiment yielding estimations of the forces acting on a Brownian particle trapped by optical tweezers. We find an increased Markov-Einstein time scale of the order of the relaxation time of the process which can be traced back to memory effects caused by the interaction of the particle and the fluid. Above the Markov-Einstein time scale, the process can be very well described by the classical overdamped Markov model for Brownian motion.Comment: 14 pages, 18 figure

H-Content Is Not Predictive of Perfluorocarbon Ocular Endotamponade Cytotoxicity in Vitro

In recent years, cases of retinal toxicity occurred in some European, Middle Eastern, and South American countries following the use of perfluorocarbon liquids (PFCLs) on vitreoretinal surgeries owing to impurities in the product. Moreover, Spanish ophthalmologists reported several toxic cases on the use of perfluoro-n-octane Ala Octa (Alamedics, Dornstadt, Germany), raising the necessity of reviewing the current validated methods used for assessing the safety of PFCLs. We proved that in samples of PFCLs contaminated on purpose with impurities previously detected in Ala Octa devices, the determination of the so-called H-content using a 1H NMR quantitative assay implemented with the electronic reference to access in vivo concentrations 2 technology failed to demonstrate a correlation between the H-content and in vitro cytotoxicity test in ARPE-19 and BALB 3T3 cell lines. Therefore, direct information on the safety of PFCLs was provided only by the cytotoxicity test in vitro validated according to ISO 10993-5, and the H-content was not predictive of perfluorocarbon ocular endotamponade cytotoxicity in vitr

Photon-electron coincidence experiments at synchrotron radiation facilities with arbitrary bunch modes

We report the adaptation of an electron–photon coincidence detection scheme to the multibunch hybrid mode of the synchrotron radiation source BESSY II (Helmholtz-Zentrum Berlin). Single-event-based data acquisition and evaluation, combined with the use of relative detection times between the coincident particles, enable the acquisition of proper coincidence signals from a quasi-continuous excitation pattern. The background signal produced by accidental coincidences in the time difference representation is modeled using the non-coincident electron and photon spectra. We validate the method by reproducing previously published results, which were obtained in the single bunch mode, and illustrate its usability for the multibunch hybrid mode by investigating the photoionization of CO2 into CO+2 B satellite states, followed by subsequent photon emission. The radiative lifetime obtained and the electron binding energy are in good agreement with earlier publications. We expect this method to be a useful tool to extend the versatility of coincident particle detection to arbitrary operation modes of synchrotron radiation facilities and other excitation sources without the need for additional experimental adjustments

Nocodazole Induced Suicidal Death of Human Erythrocytes

Background: The microtubule assembly inhibitor nocodazole has been shown to trigger caspase-independent mitotic death and caspase dependent apoptosis. Similar to apoptosis of nucleated cells, erythrocytes may undergo eryptosis, the suicidal erythrocyte death characterized by cell shrinkage and cell membrane scrambling with phosphatidylserine translocation to the erythrocyte surface. Stimulators of eryptosis include increase of cytosolic Ca2+ activity ([Ca2+]i), oxidative stress and ceramide. The present study explored, whether and how nocodazole induces eryptosis. Methods: Flow cytometry was employed to determine phosphatidylserine exposure at the cell surface from annexin-V-binding, cell volume from forward scatter, [Ca2+]i from Fluo3-fluorescence, the abundance of reactive oxygen species (ROS) from 2\u2032,7\u2032-dichlorodihydrofluorescein (DCF) diacetate dependent fluorescence as well as ceramide surface abundance utilizing specific antibodies. Tubulin abundance was quantified by TubulinTracker\u2122 Green reagent and visualized by confocal microscopy. Results: A 48 hours exposure of human erythrocytes to nocodazole ( 65 30 \u3bcg/ml) significantly increased the percentage of annexin-V-binding cells without significantly modifying average forward scatter. Nocodazole significantly increased Fluo3-fluorescence, significantly increased DCF fluorescence and significantly increased ceramide surface abundance. The effect of nocodazole on annexin-V-binding was significantly blunted, but not abolished by removal of extracellular Ca2+ and was not modified in the presence of Caspase 3 inhibitor zVAD (1 \u3bcM). Nocodazole treatment reduced the content of total tubulin. Conclusions: Nocodazole triggers cell shrinkage and phospholipid scrambling of the erythrocyte cell membrane, an effect in part due to stimulation of Ca2+ entry, oxidative stress and ceramide

Interaction of a short peptide with G-quadruplex-forming sequences: an SRCD and CD study

G-quadruplex (G4) forming DNA sequences were recently found to play a crucial role in the regulation of genomic processes such as replication, transcription and translation, also related to serious diseases. Therefore, systems capable of controlling DNA and RNA G-quadruplex structures would be useful for the modulation of various cellular events. In particular, peptides represent good candidates for targeting G-quadruplex structures, since they are easily tailored to enhance their functionality. In this work, we analyzed, by circular dichroism and synchrotron radiation circular dichroism spectroscopies, the interaction of a 25-residue peptide deriving from RHAU helicases (Rhau25) with three G-quadruplex-forming oligonucleotide sequences, in both sodium- and potassium-containing buffers, the most relevant monovalent cations in physiological conditions. The peptide displayed greater affinity for the G4 sequences adopting a parallel structure. However, it showed the ability to also interact with antiparallel or hybrid G-quadruplex structures, inducing a conformation conversion to the parallel structure. The stability of the oligonucleotide structure alone or in presence of the Rhau25 peptide was studied by temperature melting and UV denaturation experiments, and the data showed that the interaction with the peptide stabilized the conformation of oligonucleotide sequences when subjected to stress conditions

Classification and Identification of Bacteria by Mass Spectrometry and Computational Analysis

Background: In general, the definite determination of bacterial species is a tedious process and requires extensive manual labour. Novel technologies for bacterial detection and analysis can therefore help microbiologists in minimising their efforts in developing a number of microbiological applications. Methodology: We present a robust, standardized procedure for automated bacterial analysis that is based on the detection of patterns of protein masses by MALDI mass spectrometry. We particularly applied the approach for classifying and identifying strains in species of the genus Erwinia. Many species of this genus are associated with disastrous plant diseases such as fire blight. Using our experimental procedure, we created a general bacterial mass spectra database that currently contains 2800 entries of bacteria of different genera. This database will be steadily expanded. To support users with a feasible analytical method, we developed and tested comprehensive software tools that are demonstrated herein. Furthermore, to gain additional analytical accuracy and reliability in the analysis we used genotyping of single nucleotide polymorphisms by mass spectrometry to unambiguously determine closely related strains that are difficult to distinguish by only relying on protein mass pattern detection. Conclusions: With the method for bacterial analysis, we could identify fire blight pathogens from a variety of biological sources. The method can be used for a number of additional bacterial genera. Moreover, the mass spectrometry approac

A proposed potential role for increasing atmospheric CO2 as a promoter of weight gain and obesity

Human obesity has evolved into a global epidemic. Interestingly, a similar trend has been observed in many animal species, although diet composition, food availability and physical activity have essentially remained unchanged. This suggests a common factor—potentially an environmental factor affecting all species. Coinciding with the increase in obesity, atmospheric CO2 concentration has increased more than 40%. Furthermore, in modern societies, we spend more time indoors, where CO2 often reaches even higher concentrations. Increased CO2 concentration in inhaled air decreases the pH of blood, which in turn spills over to cerebrospinal fluids. Nerve cells in the hypothalamus that regulate appetite and wakefulness have been shown to be extremely sensitive to pH, doubling their activity if pH decreases by 0.1 units. We hypothesize that an increased acidic load from atmospheric CO2 may potentially lead to increased appetite and energy intake, and decreased energy expenditure, and thereby contribute to the current obesity epidemic

The {\eta}'-carbon potential at low meson momenta

The production of $\eta^\prime$ mesons in coincidence with forward-going protons has been studied in photon-induced reactions on $^{12}$C and on a liquid hydrogen (LH$_2$) target for incoming photon energies of 1.3-2.6 GeV at the electron accelerator ELSA. The $\eta^\prime$ mesons have been identified via the $\eta^\prime\rightarrow \pi^0 \pi^0\eta \rightarrow 6 \gamma$ decay registered with the CBELSA/TAPS detector system. Coincident protons have been identified in the MiniTAPS BaF$_2$ array at polar angles of $2^{\circ} \le \theta _{p} \le 11^{\circ}$. Under these kinematic constraints the $\eta^\prime$ mesons are produced with relatively low kinetic energy ($\approx$ 150 MeV) since the coincident protons take over most of the momentum of the incident-photon beam. For the C-target this allows the determination of the real part of the $\eta^\prime$-carbon potential at low meson momenta by comparing with collision model calculations of the $\eta^\prime$ kinetic energy distribution and excitation function. Fitting the latter data for $\eta^\prime$ mesons going backwards in the center-of-mass system yields a potential depth of V = $-$(44 $\pm$ 16(stat)$\pm$15(syst)) MeV, consistent with earlier determinations of the potential depth in inclusive measurements for average $\eta^\prime$ momenta of $\approx$ 1.1 GeV/$c$. Within the experimental uncertainties, there is no indication of a momentum dependence of the $\eta^\prime$-carbon potential. The LH$_2$ data, taken as a reference to check the data analysis and the model calculations, provide differential and integral cross sections in good agreement with previous results for $\eta^\prime$ photoproduction off the free proton.Comment: 9 pages, 13 figures. arXiv admin note: text overlap with arXiv:1608.0607

The N(1520) 3/2- helicity amplitudes from an energy-independent multipole analysis based on new polarization data on photoproduction of neutral pions

New data on the polarization observables T, P, and H for the reaction $\gamma p \to p\pi^0$ are reported. The results are extracted from azimuthal asymmetries when a transversely polarized butanol target and a linearly polarized photon beam are used. The data were taken at the Bonn electron stretcher accelerator ELSA using the CBELSA/TAPS detector. These and earlier data are used to perform a truncated energy-independent partial wave analysis in sliced-energy bins. This energy-independent analysis is compared to the results from energy-dependent partial wave analyses