Farmers' management of rice varietal diversity in the mid-hills of Nepal: implications for on-farm conservation and crop improvement

Season-long monitoring of on-farm rice (Oryza sativa, L.) plots in Nepal explored farmers' decision-making process on the deployment of varieties to agroecosystems, application of production inputs to varieties, agronomic practices and relationship between economic return and area planted per variety. Farmers deploy varieties [landraces (LRs) and modern varieties (MVs)] to agroecosystems based on their understanding of characteristics of varieties and agroecosystems, and the interaction between them. In marginal growing conditions, LRs can compete with MVs. Within an agroecosystem, economic return and area planted to varieties have positive relationship, but this is not so between agroecosystems. LRs are very diverse on agronomic and economic traits; therefore, they cannot be rejected a priori as inferior materials without proper evaluation. LRs have to be evaluated for useful traits and utilized in breeding programmes to generate farmer-preferred materials for marginal environments and for their conservation on-farm

Probing microplasticity in small scale FCC crystals via Dynamic Mechanical Analysis

In small-scale metallic systems, collective dislocation activity has been correlated with size effects in strength and with a step-like plastic response under uniaxial compression and tension. Yielding and plastic flow in these samples is often accompanied by the emergence of multiple dislocation avalanches. Dislocations might be active pre-yield, but their activity typically cannot be discerned because of the inherent instrumental noise in detecting equipment. We apply Alternate Current (AC) load perturbations via Dynamic Mechanical Analysis (DMA) during quasi-static uniaxial compression experiments on single crystalline Cu nano-pillars with diameters of 500 nm, and compute dynamic moduli at frequencies 0.1, 0.3, 1, and 10 Hz under progressively higher static loads until yielding. By tracking the collective aspects of the oscillatory stress-strain-time series in multiple samples, we observe an evolving dissipative component of the dislocation network response that signifies the transition from elastic behavior to dislocation avalanches in the globally pre-yield regime. We postulate that microplasticity, which is associated with the combination of dislocation avalanches and slow viscoplastic relaxations, is the cause of the dependency of dynamic modulus on the driving rate and the quasi-static stress. We construct a continuum mesoscopic dislocation dynamics model to compute the frequency response of stress over strain and obtain a consistent agreement with experimental observations. The results of our experiments and simulations present a pathway to discern and quantify correlated dislocation activity in the pre-yield regime of deforming crystals.Comment: 5 pages, 3 figure

Probing the cosmic distance duality relation using time delay lenses

The construction of the cosmic distance-duality relation (CDDR) has been widely studied. However, its consistency with various new observables remains a topic of interest. We present a new way to constrain the CDDR $\eta(z)$ using different dynamic and geometric properties of strong gravitational lenses (SGL) along with SNe Ia observations. We use a sample of $102$ SGL with the measurement of corresponding velocity dispersion $\sigma_0$ and Einstein radius $\theta_E$. In addition, we also use a dataset of $12$ two image lensing systems containing the measure of time delay $\Delta t$ between source images. Jointly these two datasets give us the angular diameter distance $D_{A_{ol}}$ of the lens. Further, for luminosity distance, we use the $740$ observations from JLA compilation of SNe Ia. To study the combined behavior of these datasets we use a model independent method, Gaussian Process (GP). We also check the efficiency of GP by applying it on simulated datasets, which are generated in a phenomenological way by using realistic cosmological error bars. Finally, we conclude that the combined bounds from the SGL and SNe Ia observation do not favor any deviation of CDDR and are in concordance with the standard value ($\eta=1$) within $2\sigma$ confidence region, which further strengthens the theoretical acceptance of CDDR.Comment: 15 Pages, 7 Figures, Accepted for publication in JCA

Structural and functional characterisation of novel bacterial Toll/Interleukin-1 receptor (TIR)-like proteins.

The extracellular domain of Toll-like receptors (TLRs) recognises highly specific pathogen-associated molecular patterns in innate immunity. This causes molecular rearrangement of the intracellular Toll/Interleukin-1 (TIR) domains of the TLRs allowing recruitment of downstream adaptor proteins via heterotypic TIR-TIR protein interactions. This in turn initiates a signalling cascade leading to proinflammatory immune responses. Recent work has indicated that TIR-like proteins (TLPs)from pathogenic bacteria contain TIR domains and interfere with host TLR signalling. Bacterial TLPs are suggested to bind to the TIR domains of host TLRs and/or adaptor proteins, thereby inhibiting intracellular signalling. This project focuses on characterisation of the TLPs from the highly pathogenic bacteria Yersinia pestis (YpTLP) and Burkholderia pseudomallei (BpTLP). The aim of the project was to produce soluble, pure and stable TLPs of yields suitable for functional and structural studies. Bacterial TLPs were expressed in E. coli. Expression of the full-length YpTLP and BpTLP using pWaldo-GFPe yielded 2.78 mg/l and 2.52 mg/l respectively. Protein purification steps were complicated by protein precipitation, possible degradation and misfolding. Subsequent efforts focused on the expression of the TIR only domain/homologue regions: YpTIR and BpTIR. Soluble YpTIR and BpTIR were expressed using pET26b. GST pull down assays indicated positive interactions between His-tagged YpTIR/BpTIR and GST-tagged human MyD88-TIR, a major adaptor protein, revealing MyD88 as a potential target of the bacterial TLPs. However expression yields of pure protein were too low to allow further studies. YpTIR and BpTIR were then expressed as fusions with an N-terminal GB1 tag using GEV2. Subsequent purification produced highly pure GB1-YpTIR (5 mg/l). NMR analysis indicated that the protein was folded and likely to be in a dimeric form, a finding confirmed by gel filtration. Native and derivative crystals of YpTIR were obtained, and native diffraction datasets collected to 2.95 A. Further work includes obtaining the phase information. It is anticipated that the crystal structure of YpTIR will provide insight into the molecular basis of TIR signalling and evidence of evolutionary conservation among TIR domains

Leveraging legacy codes to distributed problem solving environments: A web service approach

This paper describes techniques used to leverage high performance legacy codes as CORBA components to a distributed problem solving environment. It first briefly introduces the software architecture adopted by the environment. Then it presents a CORBA oriented wrapper generator (COWG) which can be used to automatically wrap high performance legacy codes as CORBA components. Two legacy codes have been wrapped with COWG. One is an MPI-based molecular dynamic simulation (MDS) code, the other is a finite element based computational fluid dynamics (CFD) code for simulating incompressible Navier-Stokes flows. Performance comparisons between runs of the MDS CORBA component and the original MDS legacy code on a cluster of workstations and on a parallel computer are also presented. Wrapped as CORBA components, these legacy codes can be reused in a distributed computing environment. The first case shows that high performance can be maintained with the wrapped MDS component. The second case shows that a Web user can submit a task to the wrapped CFD component through a Web page without knowing the exact implementation of the component. In this way, a user’s desktop computing environment can be extended to a high performance computing environment using a cluster of workstations or a parallel computer

Angular instability due to radiation pressure in the LIGO gravitational-wave detector

We observed the effect of radiation pressure on the angular sensing and control system of the Laser Interferometer Gravitational-Wave Observatory (LIGO) interferometer’s core optics at LIGO Hanford Observatory. This is the first measurement of this effect in a complete gravitational-wave interferometer. Only one of the two angular modes survives with feedback control, because the other mode is suppressed when the control gain is sufficiently large. We developed a mathematical model to understand the physics of the system. This model matches well with the dynamics that we observe