Land and water productivity of wheat in the Western Indo-Gangetic Plains of India and Pakistan: a comparative analysis

Wheat / Crop yield / Productivity / Climate / Irrigation canals / Watercourses / Water distribution / Water allocation / Policy / India / Pakistan / Gangetic Plains / Kaithal Irrigation Circle / Bhakra Canal / Chaj Sub-Basin / Lower Jehlum Canal

A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress

Background Functional annotations of large plant genome projects mostly provide information on gene function and gene families based on the presence of protein domains and gene homology, but not necessarily in association with gene expression or metabolic and regulatory networks. These additional annotations are necessary to understand the physiology, development and adaptation of a plant and its interaction with the environment. Results RiceCyc is a metabolic pathway networks database for rice. It is a snapshot of the substrates, metabolites, enzymes, reactions and pathways of primary and intermediary metabolism in rice. RiceCyc version 3.3 features 316 pathways and 6,643 peptide-coding genes mapped to 2,103 enzyme-catalyzed and 87 protein-mediated transport reactions. The initial functional annotations of rice genes with InterPro, Gene Ontology, MetaCyc, and Enzyme Commission (EC) numbers were enriched with annotations provided by KEGG and Gramene databases. The pathway inferences and the network diagrams were first predicted based on MetaCyc reference networks and plant pathways from the Plant Metabolic Network, using the Pathologic module of Pathway Tools. This was enriched by manually adding metabolic pathways and gene functions specifically reported for rice. The RiceCyc database is hierarchically browsable from pathway diagrams to the associated genes, metabolites and chemical structures. Through the integrated tool OMICs Viewer, users can upload transcriptomic, proteomic and metabolomic data to visualize expression patterns in a virtual cell. RiceCyc, along with additional species-specific pathway databases hosted in the Gramene project, facilitates comparative pathway analysis. Conclusions Here we describe the RiceCyc network development and discuss its contribution to rice genome annotations. As a case study to demonstrate the use of RiceCyc network as a discovery environment we carried out an integrated bioinformatic analysis of rice metabolic genes that are differentially regulated under diurnal photoperiod and biotic stress treatments. The analysis of publicly available rice transcriptome datasets led to the hypothesis that the complete tryptophan biosynthesis and its dependent metabolic pathways including serotonin biosynthesis are induced by taxonomically diverse pathogens while also being under diurnal regulation. The RiceCyc database is available online for free access at http://www.gramene.org/pathway

Cryo-EM analysis of Ebola virus nucleocapsid-like assembly

This protocol describes the reconstitution of the filamentous Ebola virus nucleocapsid-like assembl

Simulation results for a low energy nuclear recoil yields measurement in liquid xenon using the MiX detector

Measuring the scintillation and ionization yields of liquid xenon in response to ultra-low energy nuclear recoil events is necessary to increase the sensitivity of liquid xenon experiments to light dark matter. Neutron capture on xenon can be used to produce nuclear recoil events with energies below $0.3$ keV$_\text{NR}$ via the asymmetric emission of $\gamma$ rays during nuclear de-excitation. The feasibility of an ultra-low energy nuclear recoil measurement using neutron capture was investigated for the Michigan Xenon (MiX) detector, a small dual-phase xenon time projection chamber that is optimized for a high scintillation gain. Simulations of the MiX detector, a partial neutron moderator, and a pulsed neutron generator indicate that a population of neutron capture events can be isolated from neutron scattering events. Further, the rate of neutron captures in the MiX detector was optimized by varying the thickness of the partial neutron moderator, neutron pulse width, and neutron pulse frequency.Comment: 7 pages, 5 figures. LIDINE 2022 proceeding

A PRELIMINARY STUDY ON THE PRESENCE OF-HEAVY METALS IN AQUATIC PLANTS FROM A FRESHWATER WETLAND AT KELANIYA

Aquatic plants are known for uptake of heavy metals from water and sediments. Thisvery feature qualifies these plants as wastewater treatment agents. Capacity to absorb,heavy metals however, varies among plants. Three aquatic plants, Pistia stratiotes(floating), Limnocharis jlava (rooted) and Ipomoea aqualica (rooted plant with floatingrunners) from lriyawetiya wetland at Kelaniya were tested for the presence of copper,zinc, lead, nickel, cadmium, manganese, tin and chromium in the plant tissues.P. stratiotes, L. jlava and 1. aquatica plants were collected from the inlets, outlets and themiddle part of the wetland and above heavy metal concentrations in acid-digested rootand shoot samples were measured separately using atomic absorption spectrophotometer.Tin (Sn) is the heavy metal that was found in relatively large quantities in all threeplants, and Ipomoea aquatica recorded the highest content of Sn. Next highestoccurrence was observed with Cr and the contents were highest in the rooted plant, L.jlava, indicating that the sediment loads of Cr may be greater than the load in the watercolumn. All other heavy metals occur in relatively low concentrations in all three plantspecies, indicating partly the lower loading rates of these heavy metals in Iriyawetiyawetland.Occurrence of heavy metals in the roots was generally higher than that of the shoots.Greater Cr concentrations were recorded from roots of floating species, P. stratiotes andI. aquatica than the rooted species, L. flava.Except for cadmium (in P. slratioles) and manganese (in L. flava and 1. aquaticay;content of all the other heavy metals that occur in the plants that have been collectedfrom the inlets was greater than that of those collected from the outlet, indicating thewetlands' capacity to remove heavy metals from water and sediment through plantuptake.

Decoupling algorithms from schedules for easy optimization of image processing pipelines

Using existing programming tools, writing high-performance image processing code requires sacrificing readability, portability, and modularity. We argue that this is a consequence of conflating what computations define the algorithm, with decisions about storage and the order of computation. We refer to these latter two concerns as the schedule, including choices of tiling, fusion, recomputation vs. storage, vectorization, and parallelism. We propose a representation for feed-forward imaging pipelines that separates the algorithm from its schedule, enabling high-performance without sacrificing code clarity. This decoupling simplifies the algorithm specification: images and intermediate buffers become functions over an infinite integer domain, with no explicit storage or boundary conditions. Imaging pipelines are compositions of functions. Programmers separately specify scheduling strategies for the various functions composing the algorithm, which allows them to efficiently explore different optimizations without changing the algorithmic code. We demonstrate the power of this representation by expressing a range of recent image processing applications in an embedded domain specific language called Halide, and compiling them for ARM, x86, and GPUs. Our compiler targets SIMD units, multiple cores, and complex memory hierarchies. We demonstrate that it can handle algorithms such as a camera raw pipeline, the bilateral grid, fast local Laplacian filtering, and image segmentation. The algorithms expressed in our language are both shorter and faster than state-of-the-art implementations.National Science Foundation (U.S.) (Grant 0964004)National Science Foundation (U.S.) (Grant 0964218)National Science Foundation (U.S.) (Grant 0832997)United States. Dept. of Energy (Award DE-SC0005288)Cognex CorporationAdobe System

Occurrence of Urinary Crystals among Urinary Tract Infections Suspected Paediatric Patients, Sri Lanka

Crystalluria has become one of the most vital biomarkers in urinalysis in detecting several disease conditions. It has been reported that urinary tract infections (UTI) may be the presenting sign of Urolithiasis in children. Therefore, the objective of this study was to identify and estimate the different types of crystals in the urine samples collected from UTI suspected children who admitted to the Lady Ridgeway Hospital for children, Sri Lanka. A descriptive cross-sectional study was conducted using 400 children belong to age<12 years suspected with UTI. The participants included 242 males and 158 females. The urine samples were collected prior to start antibiotics. Each sample was examined macroscopically and centrifuged at 2000 rpm for 5 minutes. The urine sediment was examined under the light microscope and different crystal types were identified and counted at x40 magnification. Out of 400 samples 82 samples (82/400) were positive for crystalluria. The crystal types present were uric acid, calcium oxalate, triple phosphate, ammonium biuate and ammonium urate. None of the samples showed abnormal crystal types. The distribution of each crystal type was as follow; uric acid 25/82, calcium oxalate 34/82, triple phosphate 12/82, ammonium biuate 7/82 and ammonium urate 4/82. The quantity of crystals per mL of urine was ranged as follow; uric acid 850-130,000, calcium oxalate 350- >250,000, triple phosphate 650-6,000, ammonium biurate and ammonium urate were presented in clumps. KEYWORDS: Crystalluria, Uric Acid, Calcium Oxalate, Triple Phosphate, Ammonium Biurate, Ammonium Urate, Urolithiasis, Urinary Tract Infections

Plant Reactome: a resource for plant pathways and comparative analysis

Plant Reactome (http://plantreactome.gramene.org/) is a free, open-source, curated plant pathway database portal, provided as part of the Gramene project. The database provides intuitive bioinformatics tools for the visualization, analysis and interpretation of pathway knowledge to support genome annotation, genome analysis, modeling, systems biology, basic research and education. Plant Reactome employs the structural framework of a plant cell to show metabolic, transport, genetic, developmental and signaling pathways. We manually curate molecular details of pathways in these domains for reference species Oryza sativa (rice) supported by published literature and annotation of well-characterized genes. Two hundred twenty-two rice pathways, 1025 reactions associated with 1173 proteins, 907 small molecules and 256 literature references have been curated to date. These reference annotations were used to project pathways for 62 model, crop and evolutionarily significant plant species based on gene homology. Database users can search and browse various components of the database, visualize curated baseline expression of pathway-associated genes provided by the Expression Atlas and upload and analyze their Omics datasets. The database also offers data access via Application Programming Interfaces (APIs) and in various standardized pathway formats, such as SBML and BioPAX

Electrospun amplified fiber optics

A lot of research is focused on all-optical signal processing, aiming to obtain effective alternatives to existing data transmission platforms. Amplification of light in fiber optics, such as in Erbium-doped fiber amplifiers, is especially important for an efficient signal transmission. However, the complex fabrication methods, involving high-temperature processes performed in highly pure environment, slow down the fabrication and make amplified components expensive with respect to an ideal, high-throughput and room temperature production. Here, we report on near infrared polymer fiber amplifiers, working over a band of about 20 nm. The fibers are cheap, spun with a process entirely carried out at room temperature, and show amplified spontaneous emission with good gain coefficients as well as low optical losses (a few cm^-1). The amplification process is favoured by the high fiber quality and low self-absorption. The found performance metrics promise to be suitable for short-distance operation, and the large variety of commercially-available doping dyes might allow for effective multi-wavelength operation by electrospun amplified fiber optics.Comment: 27 pages, 8 figure