AUGUR: Forecasting the Emergence of New Research Topics

Being able to rapidly recognise new research trends is strategic for many stakeholders, including universities, institutional funding bodies, academic publishers and companies. The literature presents several approaches to identifying the emergence of new research topics, which rely on the assumption that the topic is already exhibiting a certain degree of popularity and consistently referred to by a community of researchers. However, detecting the emergence of a new research area at an embryonic stage, i.e., before the topic has been consistently labelled by a community of researchers and associated with a number of publications, is still an open challenge. We address this issue by introducing Augur, a novel approach to the early detection of research topics. Augur analyses the diachronic relationships between research areas and is able to detect clusters of topics that exhibit dynamics correlated with the emergence of new research topics. Here we also present the Advanced Clique Percolation Method (ACPM), a new community detection algorithm developed specifically for supporting this task. Augur was evaluated on a gold standard of 1,408 debutant topics in the 2000-2011 interval and outperformed four alternative approaches in terms of both precision and recall

Improving Editorial Workflow and Metadata Quality at Springer Nature

Identifying the research topics that best describe the scope of a scientific publication is a crucial task for editors, in particular because the quality of these annotations determine how effectively users are able to discover the right content in online libraries. For this reason, Springer Nature, the world's largest academic book publisher, has traditionally entrusted this task to their most expert editors. These editors manually analyse all new books, possibly including hundreds of chapters, and produce a list of the most relevant topics. Hence, this process has traditionally been very expensive, time-consuming, and confined to a few senior editors. For these reasons, back in 2016 we developed Smart Topic Miner (STM), an ontology-driven application that assists the Springer Nature editorial team in annotating the volumes of all books covering conference proceedings in Computer Science. Since then STM has been regularly used by editors in Germany, China, Brazil, India, and Japan, for a total of about 800 volumes per year. Over the past three years the initial prototype has iteratively evolved in response to feedback from the users and evolving requirements. In this paper we present the most recent version of the tool and describe the evolution of the system over the years, the key lessons learnt, and the impact on the Springer Nature workflow. In particular, our solution has drastically reduced the time needed to annotate proceedings and significantly improved their discoverability, resulting in 9.3 million additional downloads. We also present a user study involving 9 editors, which yielded excellent results in term of usability, and report an evaluation of the new topic classifier used by STM, which outperforms previous versions in recall and F-measure

A Microbe Associated with Sleep Revealed by a Novel Systems Genetic Analysis of the Microbiome in Collaborative Cross Mice.

The microbiome influences health and disease through complex networks of host genetics, genomics, microbes, and environment. Identifying the mechanisms of these interactions has remained challenging. Systems genetics in laboratory mice (Mus musculus) enables data-driven discovery of biological network components and mechanisms of host-microbial interactions underlying disease phenotypes. To examine the interplay among the whole host genome, transcriptome, and microbiome, we mapped QTL and correlated the abundance of cecal messenger RNA, luminal microflora, physiology, and behavior in a highly diverse Collaborative Cross breeding population. One such relationship, regulated by a variant on chromosome 7, was the association of Odoribacter (Bacteroidales) abundance and sleep phenotypes. In a test of this association in the BKS.Cg-Dock7m +/+ Leprdb/J mouse model of obesity and diabetes, known to have abnormal sleep and colonization by Odoribacter, treatment with antibiotics altered sleep in a genotype-dependent fashion. The many other relationships extracted from this study can be used to interrogate other diseases, microbes, and mechanisms

Deregulation of MADS-box transcription factor genes in a mutant defective in the <i>WUSCHEL-LIKE HOMEOBOX</i> gene <i>EVERGREEN</i> of <i>Petunia hybrida</i>

<p>Angiosperm inflorescences develop in two fundamentally different ways. In monopodial plants, for example in <i>Arabidopsis thaliana</i>, the flowers are initiated as lateral appendages of a central indeterminate inflorescence meristem. In sympodial plants, flowers arise by terminal differentiation of the inflorescence meristem, while further inflorescence development proceeds from new sympodial meristems that are generated at the flank of the terminal flower. We have used the sympodial model species <i>Petunia hybrida</i> to investigate inflorescence development. Here, we describe a mutant, <i>bonsai</i> (<i>bns</i>), which is defective in flower formation, inflorescence branching, and control of meristem size. Detailed microscopic analysis revealed that <i>bns</i> meristems retain vegetative charateristics including spiral phyllotaxis. Consistent with a block in flower formation, <i>bns</i> mutants exhibit a deregulated expression of various MADS-box genes. Molecular analysis revealed that the <i>bns</i> mutant carries a transposon insertion in the previously described <i>EVERGREEN</i> (<i>EVG</i>) gene, which belongs to the <i>WUSCHEL-LIKE HOMEOBOX</i> (<i>WOX</i>) transcription factor gene family. <i>EVG</i> falls in the <i>WOX9</i> subfamily, which has diverse developmental functions in angiosperms. The comparison of <i>WOX9</i> orthologues in five model species for flowering shows that these genes play functionally divergent roles in monopodial and sympodial plants, indicating that the <i>WOX9</i> regulatory node may have played an important role in the evolution of shoot architecture.</p

The major locus for mouse adenovirus susceptibility maps to genes of the hematopoietic cell surface-expressed LY6 family.

Susceptibility to mouse adenovirus type 1 is associated with the major quantitative trait locus Msq1. Msq1 was originally mapped to a 13-Mb region of mouse chromosome (Chr) 15 in crosses between SJL/J and BALB/cJ inbred mice. We have now narrowed Msq1 to a 0.75-Mb interval from 74.68 to 75.43 Mb, defined by two anonymous markers, rs8259436 and D15Spn14, using data from 1396 backcross mice. The critical interval includes 14 Ly6 or Ly6-related genes, including Ly6a (encoding Sca-1/TAP), Ly6e (Sca-2/Tsa1), Ly6g (Gr-1), and gpihbp1 (GPI-anchored high-density lipoprotein-binding protein 1), as well as the gene encoding an aldosterone synthase (Cyp11b2). The Ly6 family members are attractive candidates for virus susceptibility genes because their products are GPI-anchored membrane proteins expressed on lymphoid and myeloid cells, with proposed functions in cell adhesion and cell signaling. To determine interstrain variation in susceptibility and produce additional resources for cloning Msq1, we assayed the susceptibility phenotype of four previously untested inbred mouse strains. Susceptibility of strain 129S6/SvEvTac was subsequently localized to the Ly6 complex region, using polymorphic genetic markers on Chr 15 in a population of 271 (129S6/SvEvTac x BALB/cJ)F(1) x BALB/cJ backcross mice. We identified a major 129S6/SvEvTac susceptibility allele, Msq1(129S6), on Chr 15 in the same region as Msq1(SJL). The results indicate that a major host factor in mouse adenovirus type 1 susceptibility is likely to be a member of the Ly6 gene family