Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Study on the Interference Distribution Characteristics of the HVDC Grounding Electrode Current with Buried Pipelines Based on MoM and FEM

It is very important to calculate the interference of high voltage direct current (HVDC) grounding current with pipelines accurately and take proper protective measures to ensure energy transmission safety. There is still a lack of systematic research into related prediction methods that consider the nonlinear polarization on the interface between the soil and pipelines. In this paper, a methodology is proposed for calculating the coupling voltage and current on buried pipelines induced by grounding currents that accounts for nonlinear polarization based on the method of moments (MoM) and the finite element method (FEM). The validity of the proposed mathematical model is verified by a scale experiment. The interference distribution characteristics under different parameters are analyzed using the proposed method. The results show that the relationship between the maximum leakage current density and the electrode grounding current satisfy the linear function. The corrosion area becomes more concentrated as the grounding current increases. The corrosion area range increases substantially as the distance increases, whereas the influence degree decreases substantially. Both the maximum leakage current density and corrosion risk area are positively correlated with the soil resistivity

Spatial variations in the predation of nano-protozoa on bacteria in Lake Taihu, China

We investigated the predation of nano-protozoa (size fraction < 16 μm) on bacteria in four regions of Lake Taihu, China using the dilution method. The results showed that the growth rate of bacteria in the Meiliang Bay, Gonghu Bay, Dapu River mouth, and Lake Center was 0.613 ± 0.024 d−1, 1.015 ± 0.074 d−1, 1.324 ± 0.052 d−1, and 0.924 ± 0.034 d−1, respectively. The predation rate of nano-protozoa on bacteria at these sites was 0.733 ± 0.061 d−1, 1.245 ± 0.096 d−1, 1.930 ± 0.039 d−1, and 1.040 ± 0.025 d−1, respectively. The growth rate at the Dapu River mouth was significantly higher than that at Lake Center and Meiliang Bay, and that at Gonghu Bay was significantly higher than that at Meiliang Bay. The predation rate was significantly higher at the Dapu river mouth than in the other three regions, and the predation rate at Gonghu Bay was significantly higher than in Meiliang Bay. Wind-induced waves, nutrient levels and algal blooms may explain these variations of the nano-protozoa predation rate in Lake Taihu. Our results also indicated that the mean predation rate in Lake Taihu was higher than those of other freshwater, or marine water environments

Soil organic matter dynamics and nitrogen availability in response to site preparation and management during revegetation in tropical Central Queensland, Australia

Hosseini Bai, S ORCiD: 0000-0001-8646-6423Purpose: There is considerable interest in finding a cost-effective method of site preparation that effectively controls weeds during planting and further reduces the need for recurring herbicide applications. In this study, two weed control methods, herbicide and scalping, were examined. Both methods may have implications for soil organic matter (SOM) dynamics and nitrogen (N) which could consequently affect plant survival and vegetation establishment. This study aimed to investigate the dynamics of SOM, carbon (C) and N pools under site manipulation practices and the associated early plant survival and growth in tropical Australia. Materials and methods: A field trial was established in Central Queensland to examine the recovery of SOM, C and N pools following scalping and the alternative site preparation technique of sequential herbicide application. Both were contrasted with control plots which received neither treatment. Plant survival and growth were also monitored to improve our understanding of plant response to site preparation practices. Results and discussion: Scalped plots showed significantly lower values for labile C and N pools compared with the herbicide treatment and control. Generally, there was no significant difference between the herbicide and control for any of the parameters tested. Our observation indicated that herbicide application was significantly less effective than scalping to control weeds. A general decline in SOM parameters was observed in all the plots, including the control during the trial. Drought conditions were considered to be a major factor in the overall decline of SOM. Despite removal of the top soil, there was no significant difference in plant survival between herbicide and scalped areas (81% and 79% survival, respectively). Plant growth was not affected by the treatments in the first 6 months when weed competition in the herbicide areas and low nutrient availability in the scalped plots would have been significant factors in controlling growth rates. However, plants in the herbicide areas, irrespective of species, showed stronger growth than those in the scalped plots at week 61 when they had outgrown the weed competition. It is likely that differences in plant growth response to treatments will become negligible over time. Conclusions: Top soil removal was more effective than the use of herbicide in the long-term control of weeds. However, lower SOM and N availability in the scalped areas did not affect plant survival rates when compared with that of the herbicide areas. Whilst the preservation of soil organic matter is considered to be vital in short-term cropping systems, our results indicate that this is not the case for woody vegetation establishment and, in terms of cost and reduction of chemical use, removal of the organically rich top soil, with its accompanying seed burden may be both practical and desirable. © 2012 Springer-Verlag

Effects of Different Yeasts on Texture and Flavor of Sweet Potato Bread

In order to investigate the effects of different yeasts on the quality and flavor of sweet potato bread, the rheological properties, color, texture and flavor of sweet potato bread were compared and analyzed. The results showed that different yeasts had significant effects on the color, texture and flavor of sweet potato bread. The results of dynamic rheology showed that the G' and G" of yeast No.4 fermented dough were significantly higher than other groups(P<0.05). The hardness, chewiness, elasticity, cohesion and resilience of commercial yeast fermented bread were significantly lower than those of old yeast fermented bread(P<0.05). The L* value and W value of No.4 old dough yeast fermented bread were significantly higher than others(P<0.05). The results of electronic nose test showed that the main flavor substance of sweet potato bread fermented by 7 different yeasts was inorganic sulfide. A total of 61 volatile compounds were detected by GC-IMS, which were mainly alcohols, ketones and acids, followed by aldehydes, ethers, esters and pyridines. Principal component analysis showed that there were significant differences in volatile flavor compounds of 7 kinds of yeast fermented breads, two principal component contribution rate of 85%, indicating GC-IMS technology could distinguish bread fermented by different yeasts. To sum up, this paper made a detailed comparative analysis of the nature and flavor differences of bread fermented by different yeasts, and would provide a scientific basis for yeast selection in bread production

Low recovery of bacterial community after an extreme salinization-desalinization cycle

Abstract Background Understanding the recovery of bacterial communities after extreme environmental disturbances offers key opportunities to investigate ecosystem resilience. However, it is not yet clear whether bacterial communities can rebound to their pre-disturbance levels. To shed light on this issue, we tracked the responses of bacterial communities during an extreme salinization-desalinization cycle. Results Our results showed that salinization-up process induced an ecological succession, shifting from a community dominated by Betaproteobacteria to Gammaproteobacteria. Within the desalinization-down process, taxon-specific recovery trajectories varied profoundly, with only Gammaproteobacteria returning to their initial levels, of which Alphaproteobacteria was the most prominent member. The α-diversity indices gradually increased at oligosaline environment (0.03‰ to 3‰) and subsequently decreased profoundly at hypersaline condition (10‰ to 90‰). However, the indices did not return to pre-disturbance level along the previous trajectory observed during the desalinization. Approximately half of the original OTUs were not detected during desalinization, suggesting that the seed bank may be damaged by the hypersaline environment. Moreover, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) implied that the osmosensors’ capacity of bacterial communities was also impaired by the hypersaline condition. Conclusions These results suggested that the bacterial communities showed a low recovery after the extreme salinization-desalinization cycle

Effects of pre-planting site management on soil organic matter and microbial community functional diversity in subtropical Australia

Hosseini Bai, S ORCiD: 0000-0001-8646-6423Weed control is a key factor affecting early plant growth and establishment in revegetation projects in South-east Queensland of sub-tropical Australia. Costs associated with weed control are significant and methods which reduce establishment costs and effectively suppress weeds are of great interest. However, different methods may have implications for soil quality and fertility and require a detailed investigation. Understanding the response of soil organic matter (SOM) and microbial functional diversity to different weed control methods is crucial as they affect soil quality and nutrient availability. A field trial was established in South-east Queensland to identify the effects of three methods of weed control: (1) glyphosate, (2) a mixture of glyphosate and MCPA and (3) topsoil removal or scalping on SOM, microbial biomass, soil respiration, NH4+-N availability, potentially mineralisable N (PMN) and soil microbial community functional diversity (as assessed by carbon substrate utilisation using Biolog GN2 plates). The scalped area had lower SOM and microbial activity compared to the herbicide and control plots. There was no significant difference in water soluble organic carbon (WSOC), hot water extractable organic C (HWEOC), hot water extractable total N (HWETN) and microbial biomass C and N (MBC and MBN) between the herbicide and control plots, particularly at week 20. NH4+-N and PMN values were lower at week 20 than week 1 in the herbicide and scalping treatments. Week 20 was the end of the growing season and reduction in N availability may have been the result of decreasing temperature. Principal component analyses (PCA) from Biolog GN2 results indicated a separation in soil microbial community function in the scalped area compared to the other treatments which may have implications for soil properties in the long term.Scalping proved to be the most cost-effective method of site preparation, requiring fewer site visits for weed control compared to herbicide application. However, SOM was significantly affected by scalping due to topsoil removal and it may not be a sustainable practice in short rotation plantation establishment. Single herbicide application at field rates did not impact soil organisms but also failed to achieve proper weed control. © 2012 Elsevier B.V

Soil carbon and nitrogen dynamics in the first year following herbicide and scalping in a revegetation trial in south-east Queensland, Australia

Hosseini Bai, S ORCiD: 0000-0001-8646-6423During revegetation, the maintenance of soil carbon (C) pools and nitrogen (N) availability is considered essential for soil fertility and this study aimed to evaluate contrasting methods of site preparation (herbicide and scalping) with respect to the effects on soil organic matter (SOM) during the critical early establishment phase. Soil total C (TC), total N (TN), hot-water extractable organic C (HWEOC), hot-water extractable total N (HWETN), microbial biomass C and N (MBC and MBN), total inorganic N (TIN) and potentially mineralizable N (PMN) were measured over 53 weeks. MBC and MBN were the only variables affected by herbicide application. Scalping caused an immediate reduction in all variables, and the values remained low without any sign of recovery for the period of the study. The impact of scalping on HWETN and TIN lasted 22 weeks and stabilised afterwards. MBC and MBN were affected by both herbicide and scalping after initial treatment application and remained lower than control during the period of the study but did not decrease over time. While scalping had an inevitable impact on all soil properties that were measured, that impact did not worsen over time, and actually improved plant growth (unpublished data) while reducing site establishment costs. Therefore, it provides a useful alternative for weed control in revegetation projects where it is applied only once at site establishment and where SOM would be expected to recover as canopy closure is obtained and nutrient cycling through litterfall commences. © 2014 Springer-Verlag Berlin Heidelberg

Appraisal of 15N enrichment and 15N natural abundance methods for estimating N2 fixation by understorey Acacia leiocalyx and A. disparimma in a native forest of subtropical Australia

Hosseini Bai, S ORCiD: 0000-0001-8646-6423Purpose: It is anticipated that global climate change will increase the frequency of wildfires in native forests of eastern Australia. Understorey legumes such as Acacia species play an important role in maintaining ecosystem nitrogen (N) balance through biological N fixation (BNF). This is particularly important in Australian native forests with soils of low nutrient status and frequent disturbance of the nutrient cycles by fires. This study aimed to examine 15N enrichment and 15N natural abundance techniques in terms of their utilisation for evaluation of N2 fixation of understorey acacias and determine the relationship between species ecophysiological traits and N2 fixation. Materials and methods: A trial was established at sites 1 and 2 located at Toohey Forest, Queensland, Australia, a eucalypt-dominated native forest, to examine the determination of BNF using 15N enrichment and 15N natural abundance methods. Toohey Forest is an urban forest and subjected to frequent fuel reduction burns to protect the adjacent properties. Plant physiological status was measured to determine the relationship between physiological and N2 fixation activities. Results and discussion: Both 15N enrichment and 15N natural abundance techniques may be used to estimate N2 fixation of acacia tree species. The estimation of BNF using 15N enrichment was higher than those of the 15N natural abundance method. A grass reference plant, Themeda triandra, as well as tree reference plants provided an appropriate δ15N signal. Potential B values for Acacia spp. between -0. 3‰ and 1. 0‰ provided an acceptable BNF estimation. This suburban forest is located nearby a busy highway leading to N deposition over time with consequent negative δ15N signal. This N deposition may explain the separation between the δ15N signal of the acacias and that of the reference plants which led to the successful use of the 15N natural abundance technique. Acacia leiocalyx demonstrated greater N2 fixation as well as photosynthesis and instantaneous water use efficiency than Acacia disparimma. However, no strong relationship between plant photosynthesis and N2 fixation was observed in this study. A high within-treatment variation may have masked the relationships between plant BNF activities and photosynthesisConclusions: The 15N natural abundance technique is preferred to be used for future studies as it is simple and inexpensive compared with 15N enrichment method. The dependence of both species on BNF at site 2, where fuel reduction burning had not taken place for 8 years, suggests that the frequent burning impoverished the soil, and this has wider implications as higher fire frequencies are to be expected in other Australian ecosystems as a result of global climate change. © 2012 Springer-Verlag