Abstract

Validation of precipitation data is important for hydrological modeling. Though there are many models available, rainfall prediction is difficult due to various uncertainties. This study is an attempt to compare and assess the Coordinated Regional Climate Downscaling Experiment (CORDEX) model data and India Meteorological Department (IMD) observed gridded data over Malaprabha river basin, Karnataka state, India. Both gridded data sets were downscaled at 0.25× 0.25 resolution and then processed into a 12× 115 matrix form by using QGIS (2.18. 24) and MATLAB (R2003a). These two products were compared over the period 1961-2015 to evaluate their behavior in terms of fitness by using statistical parameters such as NSE, D, R, MAE, MBE and RMSE values. Results showed that out of 16 grid points, fourteen grid points showed medium correlation ranging between 0.30 and 0.49.

Abstract

In the present study an attempt has been made to propose the application of rice husk ash (RHA), by strengthening it using quarry waste (QW) as additive material in varying percentages of weight. Geotechnical properties of RHA and its combinations with quarry waste (RQ10, RQ20, RQ30, RQ40, RQ50 and RQ60) have been studied by performing grain size analysis, specific gravity, compaction, permeability and triaxial tests. The maximum increase in density, shear strength of RHA upon the addition of quarry waste was observed to be about 45.6% and 39%, respectively. The permeability of RHA, RQ mixes was found to be in fine sand range and hence their application as shell material in earth dam was proposed. The combination RQ50, with equal amounts of RHA and QW was found to exhibit maximum shear strength and was thus considered as the optimum mix. To assess the suitability of RQ50 as shell material in earth dam, numerical analysis of dam system was performed under seismic loading using FEM software Plaxis2D. The seismic behavior of dam system under the application of Nepal input motion was found satisfactory showing high shear resistance and safety against liquefaction. From the outcomes of laboratory and numerical investigations, RHA-QW mixture has been considered as a promising material to be used in earth dam enabling the bulk utilization of both the waste materials.

Abstract

Afghanistan is the most vulnerable to climate extremes related hazards, including droughts and floods that have caused huge impact on the socio-economic development of the country. The present study analysed the observed precipitation and temperature trends for seven agro-climatic zones of Afghanistan over the period 1951 to 2006 with Asian Precipitation-Highly-Resolved Observational Data Integration towards Evaluation of Water Resources (APHRODITE). The trend analysis was performed on daily data to test the increasing or decreasing rainfall and temperature trends using Mann-Kendall trend test for each agro-climatic zone of Afghanistan. The annual total precipitation has shown an increasing trend for the zones of South, South-West, East and Central, whereas, a decreasing trend has been observed for North, North-East and West zones of Afghanistan. The trend analysis of the precipitation with gridded data sets reveals for most parts of the Afghanistan, the rainfall has been observed to be decreasing. Whereas, an increasing trend of temperatures were observed for all seven agro-climatic zones of Afghanistan.

Abstract

In the present investigation, an attempt has been made to propose a lightweight back fill material using industrial wastes, namely quarry waste and granulated rubber. Granulated rubber was added in varying percentages (5%, 10%, 15%, 20%, 25%, and 30%) to quarry wastefor obtaining lightweight material. Laboratory investigation has been performed in the present study to examine the physical, chemical, andgeotechnical properties of quarry waste and the geotechnical behavior of quarry waste–granulated rubber (QWGR) mixes. Using granulatedrubber as additive, the unit weight of quarry waste material was found to reduce from 21.8 to14.1kN=m3for QWGR30 mix. The friction angleof quarry waste was obtained to be 51.2°, which increased by about 14° with rubber addition for the QWGR30 mix. The permeability of quarrywaste was found to improve from fine sand to coarse sand range with the granulated rubber inclusion, making it an efficient backfill material.QWGR30 mix was found to be an efficient lightweight backfill material with reduced lateral pressure by about 73% and 85% comparedto quarry waste and conventional sand, respectively. The economic savings of the project on backfill material by using QWGR30 over conven-tional sand would be around 8.35%. DOI:10.1061/(ASCE)HZ.2153-5515.0000455.© 2019 American Society of Civil Engineers.

Abstract

The Standardised Precipitation and Evapotranspiration Index (SPEI) became one of the popular drought indices in the context of increasing temperatures under global warming in recent periods. The SPEI is estimated by fitting a probability distribution for the difference between precipitation (P) and potential evapotranspiration (PET), which represents the climatic water balance. The choice of an inappropriate probability distribution may lead to bias in the index values leading to distorted drought severity. Till date, none of the studies have focused on the suitability of the probability distribution for SPEI over India. The objective of the present study is to compare and evaluate the performance of a group of candidate probability distributions over seven meteorologically homogeneous zones and all over India using high resolution (0.25°) gridded daily precipitation data from India Meteorological Department (IMD). The Kolmogorov–Smirnov (K–S) test was used to test the goodness-of-fit for (P–PET) and Akaike Information Criterion (AIC) was used to obtain the relative distribution rankings for each grid point. The results of the study suggest that Pearson type III distribution has performed better than other distributions, significantly for shorter time scales and slightly for longer time scales, for each meteorological homogeneous zone based on K–S test. Also, for shorter time scales, Pearson type III distribution has been observed to be significantly better based on AIC with 82.89% and 71.91% grid points for 3 and 6 months, respectively. However, the relative ranking by AIC revealed GEV distribution as the best fit for SPEI values all over India for longer time scales with total grid points as 50.26%, and 58.81% for 12- and 24-month time scales respectively. Pearson type III distribution for shorter time scales (3 and 6 months) and GEV distribution for longer time scales (12 and 24 months) have been identified as the best distributions for fitting SPEI for Indian case study. Comparison of GEV based SPEI with remote sensing-based drought severity index (DSI) for drought events indicated concordance for most of regions in India. Also, SPEI is evaluated to test its capability to represent seasonality and its performance has been compared with Standardised Precipitation Anomaly Index (SPAI) which is known to represent seasonality well.

Abstract

Background Drought is a severe environmental stress. It is estimated that about 50% of the world rice production is affected mainly by drought. Apart from conventional breeding strategies to develop drought-tolerant crops, innovative computational approaches may provide insights into the underlying molecular mechanisms of stress response and identify drought-responsive markers. Here we propose a network-based computational approach involving a meta-analytic study of seven drought-tolerant rice genotypes under drought stress. Results Co-expression networks enable large-scale analysis of gene-pair associations and tightly coupled clusters that may represent coordinated biological processes. Considering differentially expressed genes in the co-expressed modules and supplementing external information such as resistance/tolerance QTLs, transcription factors, network-based topological measures, we identify and prioritize drought-adaptive co-expressed gene modules and potential candidate genes. Using the candidate genes that are well-represented across the datasets as ‘seed’ genes, two drought-specific protein-protein interaction networks (PPINs) are constructed with up- and down-regulated genes. Cluster analysis of the up-regulated PPIN revealed ABA signalling pathway as a central process in drought response with a probable crosstalk with energy metabolic processes. Tightly coupled gene clusters representing up-regulation of core cellular respiratory processes and enhanced degradation of branched chain amino acids and cell wall metabolism are identified. Cluster analysis of down-regulated PPIN provides a snapshot of major processes associated with photosynthesis, growth, development and protein synthesis, most of which are shut down during drought. Differential regulation of phytohormones, e.g., jasmonic acid, cell wall metabolism, signalling and posttranslational modifications associated with biotic stress are elucidated. Functional characterization of topologically important, drought-responsive uncharacterized genes that may play a role in important processes such as ABA signalling, calcium signalling, photosynthesis and cell wall metabolism is discussed. Further transgenic studies on these genes may help in elucidating their biological role under stress conditions

Abstract

Network theory is now a method of choice to gain insights in understanding protein structure, folding and function. In combination with molecular dynamics (MD) simulations, it is an invaluable tool with widespread applications such as analyzing subtle conformational changes and flexibility regions in proteins, dynamic correlation analysis across distant regions for allosteric communications, in drug design to reveal alternative binding pockets for drugs, etc. Updated version of NAPS now facilitates network analysis of the complete repertoire of these biomolecules, i.e., proteins, protein–protein/nucleic acid complexes, MD trajectories, and RNA. Various options provided for analysis of MD trajectories include individual network construction and analysis of intermediate time-steps, comparative analysis of these networks, construction and analysis of average network of the ensemble of trajectories and dynamic cross-correlations. For protein–nucleic acid complexes, networks of the whole complex as well as that of the interface can be constructed and analyzed. For analysis of proteins, protein–protein complexes and MD trajectories, network construction based on inter-residue interaction energies with realistic edge-weights obtained from standard force fields is provided to capture the atomistic details. Updated version of NAPS also provides improved visualization features, interactive plots and bulk execution. URL: http://bioinf.iiit.ac.in/NAPS/

Abstract

Diffuse Large B-cell Lymphoma (DLBCL) is a highly heterogeneous cancer of B cells. Apart from cell-of-origin, genetic variations have been observed to contribute towards heterogeneity leading to different pathogenic mechanisms and overall survival outcomes. Various classification schemes have been proposed that may aid in risk stratification and developing new therapeutics for those who fail frontline therapy. This mini review highlights the significance of genetic variations as biomarkers for DLBCL and ease in extending it to clinical setting.

Abstract

Diffuse large B-cell lymphoma (DLBCL) is the aggressive form of haematological malignancies with relapse/refractory in ~ 40% of cases. It mostly develops due to accumulation of various genetic and epigenetic variations that contribute to its aggressiveness. Though large-scale structural alterations have been reported in DLBCL, their functional role in pathogenesis and as potential targets for therapy is not yet well understood. In this study we performed detection and analysis of copy number variations (CNVs) in 11 human DLBCL cell lines (4 activated B-cell–like [ABC] and 7 germinal-centre B-cell–like [GCB]), that serve as model systems for DLBCL cancer cell biology. Significant heterogeneity observed in CNV profiles of these cell lines and poor prognosis associated with ABC subtype indicates the importance of individualized screening for diagnostic and prognostic targets. Functional analysis of key cancer genes exhibiting copy alterations across the cell lines revealed activation/disruption of ten potentially targetable immuno-oncogenic pathways. Genome guided in silico therapy that putatively target these pathways is elucidated. Based on our analysis, five CNV-genes associated with worst survival prognosis are proposed as potential prognostic markers of DLBCL.

Abstract

Modelling the Sommerfeld radiating boundary is a major challenge appearing in the study of many engineering problems involving elastic wave propagation [1]. Particularly, in the finite element analysis of Structure-Soil-Structure-Interaction (SSSI) problems, where the soil modelling has to be truncated at a finite distance. This truncation of the model at finite boundary leads to reflection of radiating elastic waves. The reflected waves from the boundary will affect the solution and may lead to instabilities in the numerical analysis. Therefore, it is necessary to provide an artificial boundary condition that will transmit the outward propagating waves with minimum or negligible reflections. To address the radiating boundary condition problem, researchers have developed various kinds of formulations over few decades, such as: a). Local Absorbing Boundary Conditions (ABC) [2], b). Absorbing Layers techniques which includes Perfectly Matched Layers [3-4], Caughey Absorbing Layer Method (CALM) [5], Absorbing Layers by Increasing Damping (ALID) [6] c). Boundary element method [7], and d). Infinite elements [8-10]. ABC corresponds to the situation where the boundary is supported on infinitesimal dash-pots oriented normal and tangential to the boundary. Though these boundary conditions are very simple, the major drawback is they are inefficient when the wave impinges the boundary in inclined direction. The key property of a PML that distinguishes it from an ordinary absorbing material is that it is designed such that the propagating waves incident upon the PML from a bulk medium do not reflect on the interface. The CALM consists of defining the absorbing layers at the boundaries of the elastic medium under consideration but requires many absorbing layers which requires much computational time. The objective of this study is to present a method for radiating boundary conditions by using modified ABC to take the effect of viscous damping combining with ALID