Tools for knowledge acquisition within the NeuroScholar system and their application to anatomical tract-tracing data

Background

Knowledge bases that summarize the published literature provide useful online references for specific areas of systems-level biology that are not otherwise supported by large-scale databases. In the field of neuroanatomy, groups of small focused teams have constructed medium size knowledge bases to summarize the literature describing tract-tracing experiments in several species. Despite years of collation and curation, these databases only provide partial coverage of the available published literature. Given that the scientists reading these papers must all generate the interpretations that would normally be entered into such a system, we attempt here to provide general-purpose annotation tools to make it easy for members of the community to contribute to the task of data collation.

Results

In this paper, we describe an open-source, freely available knowledge management system called 'NeuroScholar' that allows straightforward structured markup of the PDF files according to a well-designed schema to capture the essential details of this class of experiment. Although, the example worked through in this paper is quite specific to neuroanatomical connectivity, the design is freely extensible and could conceivably be used to construct local knowledge bases for other experiment types. Knowledge representations of the experiment are also directly linked to the contributing textual fragments from the original research article. Through the use of this system, not only could members of the community contribute to the collation task, but input data can be gathered for automated approaches to permit knowledge acquisition through the use of Natural Language Processing (NLP).

Conclusion

We present a functional, working tool to permit users to populate knowledge bases for neuroanatomical connectivity data from the literature through the use of structured questionnaires. This system is open-source, fully functional and available for download from [1].

     

Collaboration and distances between German immunological institutes – a trend analysis

Background

The hypothesis that distance matters but that in recent years geographical proximity has become less important for research collaboration was tested. We have chosen a sample–authors at German immunological institutes–that is relatively homogeneous with regard to research field, language and culture, which beside distance are other possible factors influencing the willingness to co-operate. We analyse yearly distributions of co-authorship links between institutes and compare them with the yearly distributions of distances of all institutes producing papers in journals indexed in the Science Citation Index, editions 1992 till 2002. We weight both types of distributions properly with paper numbers.

Results

One interesting result is that place matters but if a researcher has to leave the home town to find a collaborator distance does not matter any longer. This result holds for all years considered, but is statistically most significant in 2002. The tendency to leave the own town for collaborators has slightly increased in the sample. In addition, yearly productivity distributions of institutes have been found to be lognormal.

Conclusion

The Internet did not change much the collaboration patterns between German immunological institutes.

     

Effects of rice straw,biochar and mineral fertiliser on methane (CH<Subscript>4</Subscript>) and nitrous oxide (N<Subscript>2</Subscript>O) emissions from rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) grown in a rain-fed lowland rice soil of Cambodia: a pot experiment

We studied the effects of water regimes and nutrient amendments on CH₄ and N₂O emissions in a 2 × 3 factorial, completely randomised growth chamber experiment. Treatments included continuously flooded (CF) and alternate wetting and drying (AWD), and three organic amendments: no amendment-control, rice straw (RS) and biochar (BC). Compound fertiliser was applied to all treatments. Rice was grown in columns packed with a paddy soil from Cambodia. Results revealed faster mineralisation of organic carbon (RS and BC) when applied in water-saturated conditions lasting for 2 weeks instead of flooding. This resulted in lower total CH₄ emissions in treatments under AWD than those under the CF water regime, namely 44 % in RS treatments and 29 % in BC treatments. Nitrous oxide fluxes were generally non-detectable during the experimental period except after fertilisation events, and the total N₂O–N emissions accounted for on average 1.7 % of the total applied mineral fertiliser N. Overall, the global warming potentials (GWPs) were lower in treatments under AWD than those under the CF water regime except for the control treatment with only mineral fertiliser application. Grain yields were slightly higher in treatments under AWD than the CF water regime. Hence, the yield-scaled GWP was also lower in the treatments under the AWD water regime, namely 51 % in RS, 59 % in BC and 17 % in control treatments. Control treatments had the lowest GWP, but provided the highest yield. The yield-scaled GWP under these treatments was therefore lower than under the other treatments.     

Integrated effect of population and weed management regimes on weed dynamics,performance, and productivity of basmati rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

Weeds caused serious problem on yield reduction of basmati rice worldwide. Losses caused by weeds varied from one country to another, depending on the presence of dominant weeds and the control methods practiced by farmers; therefore, suitable plant population and weed management practices should be adopted. Keeping these in mind, a field experiment was carried out during kharif seasons of 2009 and 2010 at crop Research Centre of SVPUA&T, Meerut, India comprising 4 planting geometries, viz. 20, 30, 40, and 50 hills m^?2 as main plot factor, and 5 weed management practices (Butachlor @ 1.0 kg ha^?1, Butachlor @ 1.0 kg ha^?1 fb (followed by) one hand weeding, Butachlor @ 1.0 kg ha^?1 fb Almix @ 4 g ha^?1, two hand weedings and weedy check) in a split plot design with 3 replications. Experimental results revealed that plant population of 50 hills m^?2 proved superior over that of 20 hills m^?2 in respect of weed density, weed dry weight, number of tillers m^?2, yield attributes, grain, straw, and biological yields. The maximum grain yield (29.00 and 31.00 q ha^?1) and straw yield (51.30 and 52.50 q ha^?1) were recorded in 50 hills m^?2 followed by 40 hills m^?2 during 2009 and 2010, respectively. In respect of nitrogen, phosphorus, and potassium removal, a reverse trend was observed: the highest in 20 hills m^?2 followed by 30, 40, and 50 hills m^?2. As far as the weed management practices are concerned, both chemical and mechanical methods of weed control were found superior over weedy check. The lowest weed density, dry weight, and highest weed control efficiency, maximum length of panicle^?1, number of panicle (m²), and 1000-grain weight and grain yield of 30.40 and 32.60 q ha^?1 were recorded with two hand weedings which was at par with Butachlor @ 1.0 kg ha^?1 fb one hand weeding over rest of the weed management practices.     

Extraction of rice-planting area and identification of chilling damage by remote sensing technology: a case study of the emerging rice production region in high latitude

Rice is the second largest staple crop in the world and therefore plays an important role in food security. As a thermophilic crop, rice is sensitive to temperature changes. Thus, research on the chilling damage of rice is essential. The Sanjiang Plain is an emerging rice production area and is located at high latitudes in China, the world’s largest rice-producing country. Landsat data were used to extract rice-planting area from 1985 to 2015. MODIS 13Q1, which was uniformly distributed during the growing period of rice, was used to obtain NDVI values of paddies during 2002–2015. Dynamic Identification Index of sterile-type chilling damage and monitoring standard of delayed-type chilling damage were the proposed methods used in this paper, which were used to judge the chilling damage of rice. The results show that in the study region, the rice-planting area in 2015 is nearly 12 times larger than that in 1985. Delayed-type chilling damage occurred in 2002 and 2009, while sterile-type chilling damage occurred in 2005, 2006, 2009, 2010, 2014, and 2015. Comparing with the prevalent meteorological standards, the results indicate that the index and standards proposed in this paper are precise, applicable, and more sensitive than them. The method is a macroscopic and accurate method to identify chilling damage in rice and can also provide a scientific basis to ensuring the stability of rice yield.     

Investigating the reduction of sodium adsorption ratio from agricultural waste by rice husk in batch scale and physical model of drain envelop

Sodium adsorption ratio (SAR) is one of the water quality indexes that whose is important due to reuse or depletion to environment. Solutes in drain water can be controlled by adsorption, chemical or biological reaction, organic envelope of drainage. Rice husk is the common option of drainage envelops in paddy fields. In this study, the ability of reduction of SAR by rice husk was evaluated in batch scale and physical model of drain envelops. In the batch experiments, the adsorption of SAR parameters was investigated by adding 2 g of rice husk into a 100 ml of sodium chloride solution. The results indicated that rice husk absorbed calcium, magnesium and sodium, respectively. By increasing the temperature, contact time and pH, adsorption of calcium, magnesium and sodium was increased; however, the higher concentration of sodium in soil solution reduced the percentage of adsorption. In a more realistic state, physical models of subsurface drainage in the paddy fields were made. Drainage envelope treatments included of rice husk (H), combination of 20 and 60 % of husk with gravel (H₂₀G₈₀ and H₆₀G₄₀) and a pipe without envelope (NE). Due to higher drain discharge and more sodium removal (lower SAR in drain water), treatment H with the discharge of 16.2 ml/min and SAR of 1.27 (meq/l)^0.5 was better in comparison with other treatments.     

High water content silk protein-based hydrogels with tunable elasticity fabricated via a Ru(II) mediated photochemical cross-linking method

Silk is very promising in the field of biomaterials as a natural biomacromolecule. Silk protein can be made into various forms of materials, including hydrogels. However, silk protein-based hydrogels have not attracted much attention due to its weak mechanical properties. Here, we report high water content silk protein-based hydrogels with tunable elasticity which were fabricated through Ru(II) mediated photochemically cross-linking tyrosine residues in regenerated silk protein. The regenerated silk protein was characterized by Fourier transform infrared spectroscopy (FTIR). The gelation kinetics of the silk protein was studied by rheology measurements. The compressive mechanical properties of the silk protein-based hydrogels was investigated using compressive tests and dynamic mechanical analysis (DMA). Compressive modulus of the hydrogels reached 349±64 MPa at 15 % strain. The fabricated silk protein-based hydrogels were also characterized by Scanning electron microscopy (SEM), revealing an interconnected porous network structure, typical of hydrogels, with an average pore size of approximately 130 μm. Finally, biocompatibility of the silk protein-based hydrogels was demonstrated through cell culture studies using a human fibroblast cell line, HFL1. The reported silk protein-based hydrogels represent a promising candidate for biomaterial applications.     

How Long can Rogued Potato Plants Left in the Field Be a Source of <Emphasis Type="Italic">Potato Virus Y</Emphasis> for Aphids?

Removal of diseased plants (roguing) is commonly practiced in seed potato production. Diseased plants left to desiccate in fields could possibly serve as sources of Potato virus Y (PVY). PVY acquisition by three aphid species (Myzus persicae, Rhopalosiphum padi, Aphis fabae) was evaluated with leaflets from rogued plants for seven days. Results showed greater PVY acquisition rates in non-colonizing aphids species compared to colonizing ones. The proportion of aphids leaving leaflets increased with time (i.e. days after plants were uprooted) and some aphids were carrying PVY in their stylets on each of the seven days of the experiment, suggesting that aphids were able to probe and acquire PVY even when plants wilted. These results confirmed that diseased plants left in fields can serve as a source of PVY for aphids even after they wilted and emphasises that proper actions must be taken to efficiently remove diseased plants from fields.     

Effectiveness of Combined Use of Mineral Oil and Insecticide Spray in Reducing <Emphasis Type="Italic">Potato Virus Y</Emphasis> (PVY) Spread under Field Conditions in New Brunswick,Canada

In the 2014 and 2015 crop seasons, the efficacies of different types, rates and combinations of mineral oil and insecticide foliar sprays for reducing Potato virus Y (PVY) spread were tested in controlled field trials in New Brunswick (NB), Canada. Experimental plots were planted with certified PVY-free Goldrush, supplemented with known virus-infected seed to raise PVY inoculum to 2.3% and 3% at the beginning of the 2014 and 2015 seasons, respectively. Treatments consisted of mineral oil-only sprays at different application rates, insecticide-only sprays of differing numbers, and several combined mineral oil and insecticide spray regimes, all compared to a no-spray control treatment. PVY spread to 18% (2014) and 22% (2015) of initially virus-free plants in no-spray control plots, with significant reductions observed in PVY spread in several treatments. Greatest PVY reductions, as low as 4% (2014) and 12% (2015), were in combined mineral oil and insecticide spray treatments, followed by oil-only sprays; while insecticide-only sprays did not significantly reduce PVY spread. As well as measuring PVY spread to marked test plants and randomly collected post-harvest tuber sample from the plots, exhibited similar treatment pattern for PVY incidence. Multiple logistic regression modeling confirmed the relative efficacy of combined oil and insecticide sprays for reducing PVY spread, while accounting for variable inoculum and aphid factors. Modeling also highlighted the importance of planting low-PVY seed initially, and of early application of foliar sprays. Local best management practice recommendations for reduction of in-field PVY spread were discussed.