Optimizing planting geometry for barley-Egyptian clover intercropping system in semi-arid sub-tropical climate.

Intercropping legumes with cereals has been a common cropping system in short-season rainfed environments due to its increased productivity and sustainability. Intercropping barley (Hordeum vulgare L.) with Egyptian clover (Trifolium alexandrinum L.) could increase the grain yield of barley and improve resource use efficiency of the intercropping system. However, non-optimum planting geometry has been a hurdle in the adaptation of barley-based cropping systems. This study was aimed at optimizing the planting geometry, and assess the productivity and profitability of barley-Egyptian clover intercropping system. Ten different planting geometries, differing in number of rows of barley, width and number of irrigation furrows and planting method were tested. Intercropping barley with Egyptian clover improved 56-68% grain yield of barley compared with mono-cropped barley. Barley remained dominant crop in terms of aggressiveness, relative crowding coefficient and competitive ratio. The amount of water used was linearly increased with increasing size of barley strip from 3 to 8 rows. The highest water use efficiency (4.83 kg/cf3) was recorded for 8-row barley strip system with 120 cm irrigation furrows compared to rest of the planting geometries. In conclusion, 8-rows of barley planted on beds with Egyptian clover in 120 cm irrigation furrows had the highest net income and cost benefit ratio. Therefore, it is recommended that this planting geometry can be used for better economic returns of barley-Egyptian clover intercropping system. However, barley strips with >8 rows were not included in this study, which is limitation of the current study. Therefore, future studies with >8 barley rows in strip should be conducted to infer the economic feasibility and profitability of wider barley strips.

High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq.

Cell-type specific regulation of gene expression requires the activation of promoters by distal genomic elements defined as enhancers. The identification and the characterization of enhancers are challenging in mammals due to their genome complexity. Here we develop CapStarr-Seq, a novel high-throughput strategy to quantitatively assess enhancer activity in mammals. This approach couples capture of regions of interest to previously developed Starr-seq technique. Extensive assessment of CapStarr-seq demonstrates accurate quantification of enhancer activity. Furthermore, we find that enhancer strength is associated with binding complexity of tissue-specific transcription factors and super-enhancers, while additive enhancer activity isolates key genes involved in cell identity and function. The CapStarr-Seq thus provides a fast and cost-effective approach to assess the activity of potential enhancers for a given cell type and will be helpful in decrypting transcription regulation mechanisms.

Assessment of computerized treatment planning system accuracy in calculating wedge factors of physical wedged fields for 6 MV photon beams.

Wedge filters are commonly used in external beam radiotherapy to achieve a uniform dose distribution within the target volume. The main objective of this study was to investigate the accuracy of the beam modifier algorithm of Theraplan plus (TPP version 3.8) treatment planning system and to confirm that either the beam hardening, beam softening and attenuation coefficients along with wedge geometry and measured wedge factor at single depth and multiple fields sizes can be the replacement of wedged profile and wedged cross-sectional data or not. In this regard the effect of beam hardening and beam softening was studied with physical wedges for 6 MV photons. The Normalized Wedge Factors (NWFs) were measured experimentally as well as calculated with the Theraplan plus, as a function of depth and field size in a water phantom for 15°, 30°, 45°, and 60° wedge filters. The beam hardening and softening was determined experimentally by deriving the required coefficients for all wedge angles. The TPP version 3.8 requires wedge transmission factor at single depth and multiple field sizes. Without incorporating the hardening and softening coefficients the percent difference between measured and calculated NFWs was as high as 7%. After the introduction of these parameters into the algorithm, the agreement between measured and TPP (V 3.8) calculated NWFs were improved to within 2 percent for various depths. Similar improvement was observed in TPP version 3.8 while calculating NWFs for various field sizes when the required coefficients were adjusted. In conclusion, the dose calculation algorithm of TPP version 3.8 showed good accuracy for a 6 MV photon beam provided beam hardening and softening parameters are taken into account. From the results, it is also concluded that, the beam hardening, beam softening and attenuation coefficients along with wedge geometry and measured wedge factor at single depth and multiple fields sizes can be the replacement of wedged profile and wedged cross-sectional data in the TPS. The study also indicated that by ignoring the beam softening and beam hardening will result in an inaccurate dose to the target volume of the patient.