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

Type 1 Fimbriae, a Colonization Factor of Uropathogenic Escherichia coli, Are Controlled by the Metabolic Sensor CRP-cAMP

Type 1 fimbriae are a crucial factor for the virulence of uropathogenic Escherichia coli during the first steps of infection by mediating adhesion to epithelial cells. They are also required for the consequent colonization of the tissues and for invasion of the uroepithelium. Here, we studied the role of the specialized signal transduction system CRP-cAMP in the regulation of type 1 fimbriation. Although initially discovered by regulating carbohydrate metabolism, the CRP-cAMP complex controls a major regulatory network in Gram-negative bacteria, including a broad subset of genes spread into different functional categories of the cell. Our results indicate that CRP-cAMP plays a dual role in type 1 fimbriation, affecting both the phase variation process and fimA promoter activity, with an overall repressive outcome on fimbriation. The dissection of the regulatory pathway let us conclude that CRP-cAMP negatively affects FimB-mediated recombination by an indirect mechanism that requires DNA gyrase activity. Moreover, the underlying studies revealed that CRP-cAMP controls the expression of another global regulator in Gram-negative bacteria, the leucine-responsive protein Lrp. CRP-cAMP-mediated repression is limiting the switch from the non-fimbriated to the fimbriated state. Consistently, a drop in the intracellular concentration of cAMP due to altered physiological conditions (e.g. growth in presence of glucose) increases the percentage of fimbriated cells in the bacterial population. We also provide evidence that the repression of type 1 fimbriae by CRP-cAMP occurs during fast growth conditions (logarithmic phase) and is alleviated during slow growth (stationary phase), which is consistent with an involvement of type 1 fimbriae in the adaptation to stress conditions by promoting biofilm growth or entry into host cells. Our work suggests that the metabolic sensor CRP-cAMP plays a role in coupling the expression of type 1 fimbriae to environmental conditions, thereby also affecting subsequent attachment and colonization of host tissues

Histone and TK0471/TrmBL2 form a novel heterogeneous genome architecture in the hyperthermophilic archaeon Thermococcus kodakarensis

This study demonstrates that the chromosome of the hyperthermophilic archaeon Thermococcus kodakarensis is organized into a heterogeneous structure created with histone and a novel protein TK0471/TrmBL2. TK0471/TrmBL2 plays dual roles as a chromosomal protein and as a global transcriptional repressor, and it is conserved in some archaeal and bacterial species