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

Tree-oriented silviculture: a new approach for coppice stands

Tree-oriented silviculture is an innovative approach of forest management aimed at enhancing a limited number of early-selected crop trees whose growth is favored over the full rotation period by applying frequent thinning in their neighborhood. This approach was originally applied to high forests, but can also be applied to coppices to maintain or improve biodiversity by selecting valuable timber trees and/or minority species as target trees. The main limitation of this silvicultural option is the need of specialized and qualified operators in all the phases, from selection of crop trees to logging operations. In this study, experimental trials were established by the Forest Research Centre of Arezzo (Italy) to verify the suitability of this approach to different structural and enviromental conditions. In coppices characterized by fast growing species such as chestnut, tree-oriented silviculture has been applied to a limited number of crop trees (50-100 ha) to obtain more valuable and larger-sized assortments in a shorter rotation period, reducing at the same time the silvicultural costs. In mixed coppices, where the ordinary management (coppicing) was applied, the abandonment or the conversion into high forest gave rise to a progressive loss in terms of species composition. Contrastingly, thinning focused around a few (5-20) trees of sporadic species allowed to maintain a high level of biodiversity, and led to favorable conditions for growth and regeneration of these species

Opportunities for coppice management at the landscape level: the Italian experience

Coppice silviculture has a long tradition in Italy. Societal demands have led to the development of forest management techniques for integrating wood production with other kinds of forest uses and regulations have been issued to limit forest degradation. In Italy, 35% of the national forest cover is currently managed under coppice silvicultural systems that provide 66% of the annual wood production. Fuel-wood demand is increasing and a large amount of fuel-wood is currently imported in Italy. Modern coppice practices differ from those adopted in the past and may have a reduced impact on ecosystem characteristics and processes. Nevertheless, coppice silviculture has a bad reputation mostly on grounds that are beyond economic, technical and ecological rationales. Neither cessation of use nor a generalized conversion from coppice to high forest are likely to respond simultaneously to the many demands deriving from complex and articulated political and economic perspectives operating at global, European, national, regional and forest stand-level scales. Different approaches of modern silviculture to coppice successfully tested in Italy for more than a decade are illustrated. We propose to combine different options at the stand and sub-stand level, including either development without human interference or conversion to high forest, and to apply these approaches within the framework of novel forest management plans and regionally consistent administrative procedures. This bottom-up approach represents a potential solution to the socio-economic and environmental challenges affecting coppicing as a silvicultural system

Parallel Evolution of Chordate <i>Cis-</i>Regulatory Code for Development

<div><p>Urochordates are the closest relatives of vertebrates and at the larval stage, possess a characteristic bilateral chordate body plan. In vertebrates, the genes that orchestrate embryonic patterning are in part regulated by highly conserved non-coding elements (CNEs), yet these elements have not been identified in urochordate genomes. Consequently the evolution of the <i>cis-</i>regulatory code for urochordate development remains largely uncharacterised. Here, we use genome-wide comparisons between <i>C. intestinalis</i> and <i>C. savignyi</i> to identify putative urochordate <i>cis-</i>regulatory sequences. <i>Ciona</i> conserved non-coding elements (ciCNEs) are associated with largely the same key regulatory genes as vertebrate CNEs. Furthermore, some of the tested ciCNEs are able to activate reporter gene expression in both zebrafish and <i>Ciona</i> embryos, in a pattern that at least partially overlaps that of the gene they associate with, despite the absence of sequence identity. We also show that the ability of a ciCNE to up-regulate gene expression in vertebrate embryos can in some cases be localised to short sub-sequences, suggesting that functional cross-talk may be defined by small regions of ancestral regulatory logic, although functional sub-sequences may also be dispersed across the whole element. We conclude that the structure and organisation of <i>cis-</i>regulatory modules is very different between vertebrates and urochordates, reflecting their separate evolutionary histories. However, functional cross-talk still exists because the same repertoire of transcription factors has likely guided their parallel evolution, exploiting similar sets of binding sites but in different combinations.</p></div

Relative positions of CNEs in <i>Ciona</i> and vertebrate Meis genes.

<p>Pink boxes denote coding exons showing similar gene structures in all 3 genes (<i>Ciona</i> lacks the twelfth exon). Blue arrowheads denote CNE positions (with numbers above if more than 1). Green arrows indicate the most distal upstream and downstream distances of CNEs from the coding sequence in each case. Not to scale.</p

Summary of GFP reporter expression driven by ciCNEs at 48<i>Tol2</i> and co-injection strategies in zebrafish embryos.

<p>Summary of GFP reporter expression driven by ciCNEs at 48<i>Tol2</i> and co-injection strategies in zebrafish embryos.</p

Analysis of Meis_ciCNE1 and Hhex_ciCNE1 in zebrafish embryos.

<p>Meis_ciCNE1 drives GFP expression in spinal cord motor neurons (A, C) and interneurons (B, D). Confocal analysis allowed to identify morphological subtypes of interneurons (E–G) and motor neurons (H, I). Intronic Hhex_CNE1 drives GFP expression in a discrete population of blood cell precursors, possibly macrophages (J–L).</p

Functional analysis of Pax6_ciCNE2 deletion constructs.

<p>(A) Schematic representation and quantification of the constructs injected in the zebrafish embryos to examine their enhancer activity. The numbers in parentheses indicate the length of each construct. (B) View of a 48 hpf embryo injected with the full length CNE2 expressing GFP in sensory neurons (arrow). In the embryos injected with DCNE2-1 (C) or DCNE2-2 (D) GFP is detected in sensory neurons (arrow). The minimal construct DCNE2-1-2+DCNE2-2-1 (E) is able to drive GFP expression in neurons along the spinal cord (arrow).</p