Abstract

Ribonucleotide:protein interactions play crucial roles in a number of biological processes. Unlike the RNA:protein interface where van der Waals contacts are prevalent, the recognition of a single ribonucleotide such as ATP by a protein occurs predominantly through hydrogen-bonding interactions. As a first step toward understanding the role of hydrogen bonding in ribonucleotide:protein recognition, the present work employs density functional theory to provide a detailed quantum-mechanical analysis of the structural and energetic characteristics of 18 unique hydrogen-bonded pairs involving the nucleobase/nucleoside moiety of four canonical ribonucleotides and the side chains of three polar amino-acid residues (arginine, glutamine, and glutamic acid) of proteins. In addition, we model five new pairs that are till now not observed in crystallographically identified ribonucleotide:protein complexes but may be identified in complexes crystallized in the future. We critically examine the characteristics of each pair in its ribonucleotide:protein crystal structure occurrence and (gas phase and water phase) optimized intrinsic structure. We further evaluated the interaction energy of each pair and characterized the associated hydrogen bonds using a number of quantum mechanics-based relationships including natural bond orbital analysis, quantum theory atoms in molecules analysis, Iogansen relationships, Nikolaienko−Bulavin−Hovorun relationships, and noncovalent interaction−reduced density gradient analysis. Our analyses reveal rich variability in hydrogen bonds in the crystallographic as well as intrinsic structure of each pair, which includes conventional O/N−H···N/O and C−H···O hydrogen bonds as well as donor/acceptor-bifurcated hydrogen bonds. Further, we identify five combinations of nucleobase and amino acid moieties; each of which exhibits at least two alternate (i.e., multimodal) structures that interact through the same nucleobase edge. In fact, one such pair exhibits four multimodal structures; one of which

Abstract

Scientific results have revealed that autophagy is able to promote cell survival in response to endoplasmic reticulum (ER) stress, while drastic events result in apoptotic cell death. Here, we analyse the important crosstalk of life-and-death decisions from a systems biological perspective by studying the regulatory modules of the unfolded protein response (UPR). While a double-negative loop between autophagy and apoptosis inducers is crucial for the switch-like characteristic of the stress response mechanism, a positive feedback loop between ER stress sensors is also essential. Corresponding to experimental data, here, we show the dynamical significance of Gadd34-CHOP connections inside the PERK branch of the UPR. The multiple system-level feedback loops seem to be crucial for managing a robust life-and-death decision depending on the level and durability of cellular stress.

Abstract

The following corrections should be made to the original paper: In the “Eflow Estimation Based on Hydrological and Hydraulic Factors” subsection of the “Results and Discussion” section: • In the sentence beginning with “Hydrological Eflow recommendations for maintaining good health over the Yamuna River were estimated to lie between 986.4 and 2,959.3 m3=s,” “986.4 and 2,959.3 m3=s” should be replaced with “27.9 m3=s (986.4 ft3=s) and 83.8 m3=s (2,959.3 ft3=s).” • In the sentence published as, “The minimum Eflow to be maintained in the river during the dry season is 3,945.7 m3=s for the Yamuna and 5.8 m3=s for the Bhadra,” “3,945.7 m3=s” should be replaced with “111.7 m3=s (3,945.7 ft3=s).” In the Supplemental Data: • In Table S3, the values in the columns under “Eflow of Yamuna River (m3=s)” are updated. The published paper contained values in ft3=s, which are retained in brackets. The values of Eflow are converted to m3=s as shown in the revised Table S3. • In Table S5, the “Yamuna” column under “Recommended Eflow (m3=s)” contains values in ft3=s in the published paper. The values of flow are converted in m3=s as shown in the revised Table S5. The values in ft3=s are retained in brackets. • In Fig. S2(a), the y-axis label of “Discharge (cumecs)” should be replaced with “Discharge (cusecs).” The corrected Fig. S2 is provided in the Supplemental Data. In the subsection “Yamuna River (Delhi Segment)” under the section “Description of Study Regions,” “Uttaranchal” should become “Uttarakhand.” In Fig. 2(a), the labels for Drains 15 and 16 should be interchanged. The revised figure is provided herein.

Abstract

This paper proposes a system for monitoring of condition and surface of roads in developing countries like India. This system will be used by government agencies to monitor municipal activities like road laying and planning. The system utilizes a database created by geo-citizens or government workers as an input. The heavy machinery in existing systems is not an optimized solution to this problem. Some existing systems use GPS and accelerometer data for determining such artifacts. So, it is evident that there is a need for a system that generates robust, frequent and accountable geo-tagged data. We propose a new collaborative model for such a purpose by fusion of data from multiple sensors hosted on smart-phones of several active geo-citizens. The system focuses mainly on volunteered geographic information, in which users can use their respective smart-phones to collect the data required and upload it for further analysis. The server side of the system infuses this data into a PostGIS database and displays the road condition on a near real-time basis over a WebGIS. The strength of a good visualization in imparting insight to decision-makers is widely recognized. We advance the paper by assessing procured road data and displaying it in an easy to understand format. In addition to visualization, the WebGIS component also provides for timeline analysis of changes in road conditions, which may help in the improved management of road infrastructure.

Abstract

Across the world billions of dollars of damage are attributed to rodents, resulting in them being classified collectively as the biggest animal pest in the world. At a commercial scale most pest control companies employ the labour intensive approach of deploying and manually monitoring rodenticide bait stations. In this paper was present, RatSpy, a visual, low-power bait station monitoring system which wirelessly reports both on bait station levels and intruders entering the bait station. The smart bait stations report data back to a custom designed cloud platform. The system performance was evaluated under realistic field conditions (on an active cattle farm) with initial results showing significant potential in terms of reducing manual labour, improving scalability and data.

Abstract

A plethora of program analysis and optimization techniques rely on linear programming at their heart. However, such techniques are often considered too slow for production use. While today’s best solvers are optimized for complex problems with thousands of dimensions, linear programming, as used in compilers, is typically applied to small and seemingly trivial problems, but to many instances in a single compilation run. As a result, compilers do not benefit from decades of research on optimizing large-scale linear programming. We design a simplex solver targeted at compilers. A novel theory of transprecision computation applied from individual elements to full data-structures provides the computational foundation. By carefully combining it with optimized representations for small and sparse matrices and specialized small-coefficient algorithms, we (1) reduce memory traffic, (2) exploit wide vectors, and (3) use low-precision arithmetic units effectively. We evaluate our work by embedding our solver into a state-of-the-art integer set library and implement one essential operation, coalescing, on top of our transprecision solver. Our evaluation shows more than an order-of-magnitude speedup on the core simplex pivot operation and a mean speedup of 3.2x (vs. GMP) and 4.6x (vs. IMath) for the optimized coalescing operation. Our results demonstrate that our optimizations exploit the wide SIMD instructions of modern microarchitectures effectively. We expect our work to provide foundations for a future integer set library that uses transprecision arithmetic to accelerate compiler analyses

Abstract

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Abstract

Cellular processes are inherently noisy, and the selection for accurate responses in presence of noise has likely shaped signalling networks. Here, we investigate the trade-off between accuracy of information transmission and its energetic cost for a mitogen-activated protein kinase (MAPK) signalling cascade. Our analysis of the pheromone response pathway of budding yeast suggests that dose-dependent induction of the negative transcriptional feedbacks in this network maximizes the information per unit energetic cost, rather than the information transmission capacity itself. We further demonstrate that futile cycling of MAPK phosphorylation and dephosphorylation has a measurable effect on growth fitness, with energy dissipation within the signalling cascade thus likely being subject to evolutionary selection. Considering optimization of accuracy versus the energetic cost of information processing, a concept well established in physics and engineering, may thus offer a general framework to understand the regulatory design of cellular signalling systems.

Abstract

n this study, a 3D seismic response of soil deposit, soil-ash deposit and soil-ash-foundation system was investigated. Homogeneous sand deposit of 80m × 9m × 20m was initially analyzed. A pond ash layer is on top of the sand deposit with varying thicknesses and the efficiency of the pond ash layer on the sand deposit was evaluated for its best suitability. The optimum sand-ash deposit overlain by a shallow foundation has been analysed under the excitation of the Nepal (Mw:7.8) and North East India earthquake (Mw:7.5). A seismic response analysis was performed using finite element software PLAXIS3D. The finite element model adopted for the present study has been validated using 1D nonlinear ground response analysis programs. e.g. DEEPSOIL and Cyclic1D. Results of the response analysis have been determined in terms of acceleration, displacement, excess pore pressure, and excess pore pressure ratio. It was observed that, the sand-pond ash-foundation system experienced liquefaction when excited under the Nepal earthquake motion whereas it is safe against the North East India earthquake.

Abstract

ndian Musicology defines 22 distinct shrutis (microtones), 12 swa- rasthanas (semitones) and 7 swaras (tones). By implementing the mathematical concepts like cycle of fourths and fifths, these shrutis acquire a discrete frequency ratio which justifies the Bharatha’s 22 shrutis experiment. Indian classical music defines the 7 swaras and each swara is associated to an animal/bird call. The Grama system in Indian music distributes the 22 shrutis amongst the 7 swaras. We based our work on the Shadja Grama system. The traversal of pitches in a swara are more important in understanding the swara as compared to the fre- quency ratio. This shows us that swaras have peculiar properties and an identity independent of the octave.