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

Effect of Phosphorus Fertilizer and Irrigation Frequency on Yield and Protein Content of Alfalfa

Alfalfa ranks the first among forage crops in arid areas of the middle east, where irrigation water is limited, and conservation of it is of great concern. An experiment was conducted to study the effect of P fertilizer combined with irrigation intervals on yield parameters and protein content of alfalfa. During two years, three P levels (0, 25, 50 kg P /ha/cut) and two irrigation interval treatments (5,10 days) through seven cuts a year were applied. Studied parameters were forage fresh yield (FFY), forage dry yield (FDY), dry matter percentage (DM%), crude protein percentage (CP%), and crude protein yield (CPY). The results showed that increasing P application increased fresh, dry and protein yield significantly. Little decrease but significant in fresh, dry and protein yield was associated with increasing irrigation inter-vals. Increasing P fertilizer compensated for the effect of increasing irrigation intervals

Impacts of Nicotiana glauca Graham Invasion on the Vegetation Composition and Soil: A Case Study of Taif, Western Saudi Arabia

Invasive species are considered a serious problem in different ecosystems worldwide. They can compete and interfere with native plants, leading to a shift in community assembly and ecosystem function. The present study aimed to evaluate the effects of Nicotiana glauca Graham invasion on native vegetation composition and soil of the most invaded locations in the Taif region, Western Saudi Arabia, including Alwaht (WHT), Ar-Ruddaf (RDF), and Ash-shafa (SHFA). Plant species list, life span, life form, and chorotypes were assessed. Six locations highly infested with N. glauca shrubs were selected, and the morphological parameters of the shrubs were measured. Within each location, richness, evenness, relative density of species, and soil were measured either under the canopy of N. glauca shrubs or outside the canopy. Floristic analysis revealed the existence of 144 plant species, mainly perennial. The shrubs at the SHFA1 location showed the highest values of all measured morphological parameters. The WHT 1 location showed high richness and evenness, while the WHAT 2 location showed less richness and evenness. The invaded locations showed substantial variation in the community composition. Additionally, the effect of N. glauca on the understory species varied from competition to facilitation, where most of the understory species were inhibited. As an average of all locations, 65.86% of the plant species were recorded only outside the canopy of N. glauca. The vegetation analysis revealed that the SHFA location is more vulnerable to invasion that could be ascribed to its wide range of habitats and high disturbance. The soil–vegetation relationships showed significant variations among the studied locations regarding soil composition, and thereby showed a wide ecological range of the invasive shrubs N. glauca. Therefore, the invasion of N. glauca in the Taif region altered the species interactions, nutrients, and soil properties

Ecological Insight, Anatomical Features, and Fiber Characterization of <i>Leptadenia pyrotechnica</i> (Forrsk.) Decne. as a Promising Resource

Wild plants are considered promising natural eco-friendly resources for fibers. Leptadenia pyrotechnica is a xerophytic shrub that flourishes in a sandy desert habitat with high biomass production; therefore, it could be a potential resource for fibers. The present study aimed to investigate the vegetation composition of L. pyrotechnica communities and their correlation with soil variables. Additionally, this study aimed to evaluate the anatomical features of the stem as well as fiber characteristics, including chemical, biometry, morphological, and optical properties. The vegetation analysis showed the presence of 60 species belonging to 22 families, with a prevalence of therophytes. Four communities were determined, dominated by L. pyrotechnica and with co-dominance of the shrubs Haloxylon salicornicum, Ochradenus baccatus, and Retama raetam. The soil organic matter, salinity, texture, and cations were parameters that substantially affect the L. pyrotechnica community. The anatomical investigation showed the structural (anatomical) adaptation of L. pyrotechnica to arid habitats. Chemical analysis of the raw plant material revealed satisfactory levels of cellulose and hemicellulose (48.61% and 18.59%), while lignin and ash contents were relatively low, compared to hardwoods and softwoods. The fiber characterization revealed that fibesr length was 0.72 mm, while width and cell wall thickness were 20.46 and 6.48 μm, respectively. The optical properties revealed a birefringence of 0.028, indicating a good refractive index. These fiber characteristics showed that L. pyrotechnica could be used as raw material for the production of good-quality paper. A further feasibility study is recommended for the evaluation of L. pyrotechnica fibers, as a promising resource for papermaking at a large scale

Ecological Insight, Anatomical Features, and Fiber Characterization of Leptadenia pyrotechnica (Forrsk.) Decne. as a Promising Resource

Wild plants are considered promising natural eco-friendly resources for fibers. Leptadenia pyrotechnica is a xerophytic shrub that flourishes in a sandy desert habitat with high biomass production; therefore, it could be a potential resource for fibers. The present study aimed to investigate the vegetation composition of L. pyrotechnica communities and their correlation with soil variables. Additionally, this study aimed to evaluate the anatomical features of the stem as well as fiber characteristics, including chemical, biometry, morphological, and optical properties. The vegetation analysis showed the presence of 60 species belonging to 22 families, with a prevalence of therophytes. Four communities were determined, dominated by L. pyrotechnica and with co-dominance of the shrubs Haloxylon salicornicum, Ochradenus baccatus, and Retama raetam. The soil organic matter, salinity, texture, and cations were parameters that substantially affect the L. pyrotechnica community. The anatomical investigation showed the structural (anatomical) adaptation of L. pyrotechnica to arid habitats. Chemical analysis of the raw plant material revealed satisfactory levels of cellulose and hemicellulose (48.61% and 18.59%), while lignin and ash contents were relatively low, compared to hardwoods and softwoods. The fiber characterization revealed that fibesr length was 0.72 mm, while width and cell wall thickness were 20.46 and 6.48 &mu;m, respectively. The optical properties revealed a birefringence of 0.028, indicating a good refractive index. These fiber characteristics showed that L. pyrotechnica could be used as raw material for the production of good-quality paper. A further feasibility study is recommended for the evaluation of L. pyrotechnica fibers, as a promising resource for papermaking at a large scale

Evaluation of genetic diversity of Panicum turgidum Forssk from Saudi Arabia

The genetic diversity of 177 accessions of Panicum turgidum Forssk, representing ten populations collected from four geographical regions in Saudi Arabia, was analyzed using amplified fragment length polymorphism (AFLP) markers. A set of four primer-pairs with two/three selective nucleotides scored 836 AFLP amplified fragments (putative loci/genome landmarks), all of which were polymorphic. Populations collected from the southern region of the country showed the highest genetic diversity parameters, whereas those collected from the central regions showed the lowest values. Analysis of molecular variance (AMOVA) revealed that 78% of the genetic variability was attributable to differences within populations. Pairwise values for population differentiation and genetic structure were statistically significant for all variances. The UPGMA dendrogram, validated by principal coordinate analysis-grouped accessions, corresponded to the geographical origin of the accessions. Mantel’s test showed that there was a significant correlation between the genetic and geographical distances (r = 0.35, P < 0.04). In summary, the AFLP assay demonstrated the existence of substantial genetic variation in P. turgidum. The relationship between the genetic diversity and geographical source of P. turgidum populations of Saudi Arabia, as revealed through this comprehensive study, will enable effective resource management and restoration of new areas without compromising adaptation and genetic diversity

Vegetation Composition of the Halophytic Grass <i>Aeluropus lagopoides</i> Communities within Coastal and Inland Sabkhas of Saudi Arabia

Sabkhas are unique, highly saline ecosystems, where specially adapted plants can grow. Aeluropus lagopoides (L.) Thwaites is a halophytic forage plant growing in salt marsh habitats of inland and coastal sabkhas of Saudi Arabia. The present study provides an analysis of vegetation composition and distribution of the A. lagopoides community in five different regions within Saudi Arabia, emphasizing the environmental factors that affect species distribution. The floristic survey revealed the presence of 48 species, belonging to 26 families. Poaceae, Chenopodiaceae, Mimosaceae, Zygophyllaceae, and Asteraceae are the largest families (50% of total species). Phanerophyte, followed by chamaephytes, are the most frequent forms, indicating a typical saline desert life-form spectrum. The vegetation analysis revealed the dominance of A. lagopoides in all locations, where it was the most dominant species in Qareenah, Qaseem, and Salwa locations, and the second most dominant species in Jouf and Jizan locations. The flourishment of this halophytic grass within a wide soil range in sabkhas revealed its adaptability to the harsh environment, which could be ascribed to its structural adaptations and modifications, as well as the phenotypic plasticity. The Qareenah and Qaseem locations attained the highest species richness and evenness, while the Jizan location was the least diverse. Within the studied locations, other highly salt-tolerant species were determined with high abundances, such as Suaeda aegyptiaca (Hasselq.) Zohary, Zygophyllum album L.f., Tamarix nilotica (Ehrenb.) Bunge, Cressa cretica L., and Salicornia europaea L. The soil analysis showed a significant variation for all parameters among the studied locations, except for pH, chloride, and clay content. The Qaseem location revealed the highest values of most soil parameters, while the Jizan location showed the lowest. The canonical correspondence analysis (CCA) showed that the community structure and diversity are mainly affected by the soil salinity and moisture. Due to the economic potentialities of A. lagopoides as a forage plant and sand stabilizer, the conservation of its habitats is of vital importance. In addition, this grass could be integrated as a promising forage candidate that can be planted in saline-affected areas, even in the summer dry season