Emergence of robust nucleosome patterns from an interplay of positioning mechanisms

Proper positioning of nucleosomes in eukaryotic cells is determined by a complex interplay of factors, including nucleosome-nucleosome interactions, DNA sequence, and active chromatin remodeling. Yet, characteristic features of nucleosome positioning, such as geneaveraged nucleosome patterns, are surprisingly robust across perturbations, conditions, and species. Here, we explore how this robustness arises despite the underlying complexity. We leverage mathematical models to show that a large class of positioning mechanisms merely affects the quantitative characteristics of qualitatively robust positioning patterns. We demonstrate how statistical positioning emerges as an effective description from the complex interplay of different positioning mechanisms, which ultimately only renormalize the model parameter quantifying the effective softness of nucleosomes. This renormalization can be species-specific, rationalizing a puzzling discrepancy between the effective nucleosome softness of S. pombe and S. cerevisiae. More generally, we establish a quantitative framework for dissecting the interplay of different nucleosome positioning determinants

Pulsed flows at the high-altitude cusp poleward boundary, and associated ionospheric convection and particle signatures, during a cluster - FAST - SuperDARN - sondrestrom conjunction under a southwest

Particle and magnetic field observations during a magnetic conjunction Cluster 1-FAST-Søndrestrøm within the field of view of SuperDARN radars on 21 January 2001 allow us to draw a detailed, comprehensive and self-consistent picture at three heights of signatures associated with transient reconnection under a steady south-westerly IMF (clock angle ≈130◦). Cluster 1 was outbound through the high altitude (∼12RE ) exterior northern cusp tailward of the bifurcation line (geomagnetic Bx>0) when a solar wind dynamic pressure release shifted the spacecraft into a boundary layer downstream of the cusp. The centerpiece of the investigation is a series of flow bursts observed there by the spacecraft, which were accompanied by strong field pertur- bations and tailward flow deflections. Analysis shows these to be Alfven waves. We interpret these flow events as being due to a sequence of reconnected flux tubes, with field-aligned currents in the associated Alfven waves carrying stresses to the underlying ionosphere, a view strengthened by the other observations. At the magnetic footprint of the region of Cluster flow bursts, FAST observed an ion energy- latitude disperison of the stepped cusp type, with individual cusp ion steps corresponding to individual flow bursts. Simultaneously, the SuperDARN Stokkseyri radar observed very strong poleward-moving radar auroral forms (PMRAFs) which were conjugate to the flow bursts at Cluster. FAST was traversing these PMRAFs when it observed the cusp ion steps. The Søndrestrøm radar observed pulsed ionospheric flows (PIFs) just poleward of the convection reversal boundary. As at Cluster, the flow was eastward (tailward), implying a coherent eastward (tailward) motion of the hypothesized open flux tubes. The joint Søndrestrøm and FAST observations indicate that the open/closed field line boundary was equatorward of the convection reversal boundary by ∼2 deg. The unprecedented accuracy of the conjunction argues strongly for the validity of the interpretation of the various signatures as resulting from transient reconnection. In particular, the cusp ion steps arise on this pass from this origin, in consonance with the original pulsating cusp model. The observations point to the need of extending current ideas on the response of the ionosphere to transient reconnection. Specifically, it argues in favor of re-establishing the high-latitude boundary layer downstream of the cusp as an active site of momentum transfer

Evaluating the scale, growth, and origins of right-wing echo chambers on YouTube

Although it is understudied relative to other social media platforms, YouTube is arguably the largest and most engaging online media consumption platform in the world. Recently, YouTube's outsize influence has sparked concerns that its recommendation algorithm systematically directs users to radical right-wing content. Here we investigate these concerns with large scale longitudinal data of individuals' browsing behavior spanning January 2016 through December 2019. Consistent with previous work, we find that political news content accounts for a relatively small fraction (11%) of consumption on YouTube, and is dominated by mainstream and largely centrist sources. However, we also find evidence for a small but growing "echo chamber" of far-right content consumption. Users in this community show higher engagement and greater "stickiness" than users who consume any other category of content. Moreover, YouTube accounts for an increasing fraction of these users' overall online news consumption. Finally, while the size, intensity, and growth of this echo chamber present real concerns, we find no evidence that they are caused by YouTube recommendations. Rather, consumption of radical content on YouTube appears to reflect broader patterns of news consumption across the web. Our results emphasize the importance of measuring consumption directly rather than inferring it from recommendations.Comment: 29 pages, 21 figures, 15 table

Polyhedral Cosmic Strings

Quantum field theory is discussed in M\"obius corner kaleidoscopes using the method of images. The vacuum average of the stress-energy tensor of a free field is derived and is shown to be a simple sum of straight cosmic string expressions, the strings running along the edges of the corners. It does not seem possible to set up a spin-half theory easily.Comment: 15 pages, 4 text figures not include

Acceleration of Solar Wind Ions by Nearby Interplanetary Shocks: Comparison of Monte Carlo Simulations with Ulysses Observations

The most stringent test of theoretical models of the first-order Fermi mechanism at collisionless astrophysical shocks is a comparison of the theoretical predictions with observational data on particle populations. Such comparisons have yielded good agreement between observations at the quasi-parallel portion of the Earth's bow shock and three theoretical approaches, including Monte Carlo kinetic simulations. This paper extends such model testing to the realm of oblique interplanetary shocks: here observations of proton and alpha particle distributions made by the SWICS ion mass spectrometer on Ulysses at nearby interplanetary shocks are compared with test particle Monte Carlo simulation predictions of accelerated populations. The plasma parameters used in the simulation are obtained from measurements of solar wind particles and the magnetic field upstream of individual shocks. Good agreement between downstream spectral measurements and the simulation predictions are obtained for two shocks by allowing the the ratio of the mean-free scattering length to the ionic gyroradius, to vary in an optimization of the fit to the data. Generally small values of this ratio are obtained, corresponding to the case of strong scattering. The acceleration process appears to be roughly independent of the mass or charge of the species.Comment: 26 pages, 6 figures, AASTeX format, to appear in the Astrophysical Journal, February 20, 199

Scaling of the Conductivity with Temperature and Uniaxial Stress in Si:B at the Metal-Insulator Transition

Using uniaxial stress to tune Si:B through the metal-insulator transition we find the conductivity at low temperatures shows an excellent fit to scaling with temperature and stress on both sides of the transition. The scaling functions yield the conductivity in the metallic and insulating phases, and allow a reliable determination of the temperature dependence in the critical regions on both sides of the transition

The Plasma and Suprathermal Ion Composition (PLASTIC) investigation on the STEREO observatories

The Plasma and Suprathermal Ion Composition (PLASTIC) investigation provides the in situ solar wind and low energy heliospheric ion measurements for the NASA Solar Terrestrial Relations Observatory Mission, which consists of two spacecraft (STEREO-A, STEREO-B). PLASTIC-A and PLASTIC-B are identical. Each PLASTIC is a time-of-flight/energy mass spectrometer designed to determine the elemental composition, ionic charge states, and bulk flow parameters of major solar wind ions in the mass range from hydrogen to iron. PLASTIC has nearly complete angular coverage in the ecliptic plane and an energy range from ∼0.3 to 80 keV/e, from which the distribution functions of suprathermal ions, including those ions created in pick-up and local shock acceleration processes, are also provided

Clinical significance of VEGF-A, -C and -D expression in esophageal malignancies

Vascular endothelial growth factors ( VEGF)- A, - C and - D are members of the proangiogenic VEGF family of glycoproteins. VEGF-A is known to be the most important angiogenic factor under physiological and pathological conditions, while VEGF-C and VEGF-D are implicated in the development and sprouting of lymphatic vessels, so called lymphangiogenesis. Local tumor progression, lymph node metastases and hematogenous tumor spread are important prognostic factors for esophageal carcinoma ( EC), one of the most lethal malignancies throughout the world. We found solid evidence in the literature that VEGF expression contributes to tumor angiogenesis, tumor progression and lymph node metastasis in esophageal squamous cell carcinoma ( SCC), and many authors could show a prognostic value for VEGF-assessment. In adenocarcinoma (AC) of the esophagus angiogenic properties are acquired in early stages, particularly in precancerous lesions like Barrett's dysplasia. However, VEGF expression fails to give prognostic information in AC of the esophagus. VEGF-C and VEGF-D were detected in SCC and dysplastic lesions, but not in normal mucosa of the esophagus. VEGF-C expression might be associated with lymphatic tumor invasion, lymph node metastases and advanced disease in esophageal SCC and AC. Therapeutic interference with VEGF signaling may prove to be a promising way of anti-angiogenic co-treatment in esophageal carcinoma. However, concrete clinical data are still pending

Solar wind ion trends and signatures: STEREO PLASTIC observations approaching solar minimum

STEREO has now completed the first two years of its mission, moving from close proximity to Earth in 2006/2007 to more than 50 degrees longitudinal separation from Earth in 2009. During this time, several large-scale structures have been observed in situ. Given the prevailing solar minimum conditions, these structures have been predominantly coronal hole-associated solar wind, slow solar wind, their interfaces, and the occasional transient event. In this paper, we extend earlier solar wind composition studies into the current solar minimum using high-resolution (1-h) sampling times for the charge state analysis. We examine 2-year trends for iron charge states and solar wind proton speeds, and present a case study of Carrington Rotation 2064 (December 2007) which includes minor ion (He, Fe, O) kinetic and Fe composition parameters in comparison with proton and magnetic field signatures at large-scale structures observed during this interval