FLASH: ultra-fast protocol to identify RNA-protein interactions in cells

Determination of the in vivo binding sites of RNA-binding proteins (RBPs) is paramount to understanding their function and how they affect different aspects of gene regulation. With hundreds of RNA-binding proteins identified in human cells, a flexible, high-resolution, high-throughput, highly multiplexible and radioactivity-free method to determine their binding sites has not been described to date. Here we report FLASH (Fast Ligation of RNA after some sort of Affinity Purification for High-throughput Sequencing), which uses a special adapter design and an optimized protocol to determine protein-RNA interactions in living cells. The entire FLASH protocol, starting from cells on plates to a sequencing library, takes 1.5 days. We demonstrate the flexibility, speed and versatility of FLASH by using it to determine RNA targets of both tagged and endogenously expressed proteins under diverse conditions in vivo

Moisture dynamics in the masonry fabric of historic buildings subjected to wind-driven rain and flooding

Current climatic projections show clearly that increasingly more extreme weather events are to be expected in the future. Historic buildings are considered to be the most vulnerable to this adverse climatic impact, via moisture induced deterioration and resulting strength decay in their construction materials. Therefore, the identification of these climatic effects is important to be able to develop suitable tools to mitigate them, both for individual buildings and on a regional scale. This paper presents the analysis of a comprehensive environmental monitoring of two historic buildings in Tewkesbury, Gloucestershire, UK, to provide thorough insight on their performances under environmental loading on a comparative basis. Firstly, the effect of wind-driven rain (WDR) and flooding is assessed by correlation with relative humidity (RH) measurements. The WDR measurements are then compared against values calculated using well established semi-empirical models and reasons behind the limited correlation are discussed. The dynamic hygrothermal response of two different historic fabrics is studied in greater detail by monitoring in-wall temperature and RH. The conclusions drawn from the analysis of the monitoring outputs are then further elaborated on by using hygrothermal characterization obtained by dynamic vapour sorption (DVS) testing of material samples extracted from the fabric of these buildings. The study concludes that the current environmental conditions pose a threat on the building envelopes unless routine maintenance is provided, and that monitoring methodology devised is clearly successful in quantifying the exposure of the two historic buildings to environmental conditions, onsetting deterioration phenomena in the envelop materials

The effect of sample properties on the electron velocity in quantum Hall bars

We report on our theoretical investigation of the effects of the confining potential profile and sample size on the electron velocity distribution in (narrow) quantum-Hall systems. The electrostatic properties of the electron system are obtained by the Thomas-Fermi-Poisson nonlinear screening theory. The electron velocity distribution as a function of the lateral coordinate is obtained from the slope of the screened potential at the Fermi level and within the incompressible strips (ISs). We compare our findings with the recent experiments.Comment: 8 pages, 6 figure

Assessment of flood and wind driven rain impact on mechanical properties of historic brick masonry

As a result of increased rainfall and flooding the building fabric of historic structures in exposed areas are likely to be subject to higher and more sustained moisture content levels, along with experiencing an increased frequency and severity of wetting and drying cycles. This study aims to evaluate the impact of such cyclic wetting and drying on the mechanical behaviour of historic brick masonry. The reported results are obtained from a series of weathering and mechanical tests carried out on clay bricks and masonry specimens. The weathering test regime derives from analysis of observed weather data, combined with review of similar existing test protocols. Similarly, a modified mechanical test procedure is applied to simulate fatigue observed in the field. The results indicate that exposure to the weathering tests results in a reduction of masonry shear strength. This is discussed within the context of wider work carried out at a case study location, and highlights the value of designing a weathering regime that can more closely replicate the in-situ weathering processes. In this way the data collected in this experimental programme is shown to be suitable for use in contextual analysis of individual historic masonry case studies, with respect to climate change and the associated alteration of wetting regimes

O(alpha_s^2) QCD corrections to the electroproduction of hadrons with high transverse momentum

We compute the order alpha_s^2 corrections to the one particle inclusive electroproduction cross section of hadrons with non vanishing transverse momentum. We perform the full calculation analytically, and obtain the expression of the factorized (finite) cross section at this order. We compare our results with H1 data on forward production of pi^0, and discuss the phenomenological implications of the rather large higher order contributions obtained in that case. Specifically, we analyze the cross section sensitivity to the factorization and renormalization scales, and to the input fragmentation functions, over the kinematical region covered by data. We conclude that the data is well described by the O(alpha_s^2) predictions within the theoretical uncertainties and without the inclusion of any physics content beyond the DGLAP approach.Comment: 11 pages, LaTeX, 7 figure

Capacity Bounds and Concatenated Codes Over Segmented Deletion Channels

Cataloged from PDF version of article.We develop an information theoretic characterization and a practical coding approach for segmented deletion channels. Compared to channels with independent and identically distributed (i.i.d.) deletions, where each bit is independently deleted with an equal probability, the segmentation assumption imposes certain constraints, i.e., in a block of bits of a certain length, only a limited number of deletions are allowed to occur. This channel model has recently been proposed and motivated by the fact that for practical systems, when a deletion error occurs, it is more likely that the next one will not appear very soon. We first argue that such channels are information stable, hence their channel capacity exists. Then, we introduce several upper and lower bounds with two different methods in an attempt to understand the channel capacity behavior. The first scheme utilizes certain information provided to the transmitter and/or receiver while the second one explores the asymptotic behavior of the bounds when the average bit deletion rate is small. In the second part of the paper, we consider a practical channel coding approach over a segmented deletion channel. Specifically, we utilize outer LDPC codes concatenated with inner marker codes, and develop suitable channel detection algorithms for this scenario. Different maximum-a-posteriori (MAP) based channel synchronization algorithms operating at the bit and symbol levels are introduced, and specific LDPC code designs are explored. Simulation results clearly indicate the advantages of the proposed approach. In particular, for the entire range of deletion probabilities less than unity, our scheme offers a significantly larger transmission rate compared to the other existing solutions in the literature

The dual parameterization of the proton generalized parton distribution functions H and E and description of the DVCS cross sections and asymmetries

We develop the minimal model of a new leading order parameterization of GPDs introduced by Shuvaev and Polyakov. The model for GPDs H and E is formulated in terms of the forward quark distributions, the Gegenbauer moments of the D-term and the forward limit of the GPD E. The model is designed primarely for small and medium-size values of x_B, x_B \leq 0.2. We examined two different models of the t-dependence of the GPDs: The factorized exponential model and the non-factorized Regge-motivated model. Using our model, we successfully described the DVCS cross section measured by H1 and ZEUS, the moments of the beam-spin A_{LU}^{\sin \phi}, beam-charge A_{C}^{\cos \phi} and transversely-polarized target A_{UT}^{\sin \phi \cos \phi} DVCS asymmetries measured by HERMES and A_{LU}^{\sin \phi} measured by CLAS. The data on A_{C}^{\cos \phi} prefers the Regge-motivated model of the t-dependence of the GPDs. The data on A_{UT}^{\sin \phi \cos \phi} indicates that the u and d quarks carry only a small fraction of the proton total angular momentum.Comment: 33 pages, 11 figure

Wind Driven Rain (WDR) Laboratory Tests on Cavity Wall Specimens treated with surface waterproofing products

Wind driven rain (WDR) is one of the most common sources of moisture risks affecting buildings in the UK. Water penetration can lead to defects such as ineffective insulation, damp inner walls and freeze-thaw damage, causing issues in both energy efficiency and wall integrity. Surface waterproofing products have shown great potential as a new method of improving the moisture condition in buildings. This paper is focused on real size cavity walls tested under WDR exposure to study the hygrothermal performance of surface waterproofing products. Test results show both acrylic-based liquid and silane/siloxane blend cream products were capable of lessening moisture enrichment of masonry cavity walls under cyclic WDR loading