Entity Linking and Discovery via Arborescence-based Supervised Clustering

Previous work has shown promising results in performing entity linking by measuring not only the affinities between mentions and entities but also those amongst mentions. In this paper, we present novel training and inference procedures that fully utilize mention-to-mention affinities by building minimum arborescences (i.e., directed spanning trees) over mentions and entities across documents in order to make linking decisions. We also show that this method gracefully extends to entity discovery, enabling the clustering of mentions that do not have an associated entity in the knowledge base. We evaluate our approach on the Zero-Shot Entity Linking dataset and MedMentions, the largest publicly available biomedical dataset, and show significant improvements in performance for both entity linking and discovery compared to identically parameterized models. We further show significant efficiency improvements with only a small loss in accuracy over previous work, which use more computationally expensive models.Comment: Updated reference

Regulation of antibiotic production in Actinobacteria: new perspectives from the post-genomic era

The antimicrobial activity of many of their natural products has brought prominence to the Streptomycetaceae, a family of Gram-positive bacteria that inhabit both soil and aquatic sediments. In the natural environment, antimicrobial compounds are likely to limit the growth of competitors, thereby offering a selective advantage to the producer, in particular when nutrients become limited and the developmental programme leading to spores commences. The study of the control of this secondary metabolism continues to offer insights into its integration with a complex lifecycle that takes multiple cues from the environment and primary metabolism. Such information can then be harnessed to devise laboratory screening conditions to discover compounds with new or improved clinical value. Here we provide an update of the review we published in NPR in 2011. Besides providing the essential background, we focus on recent developments in our understanding of the underlying regulatory networks, ecological triggers of natural product biosynthesis, contributions from comparative genomics and approaches to awaken the biosynthesis of otherwise silent or cryptic natural products. In addition, we highlight recent discoveries on the control of antibiotic production in other Actinobacteria, which have gained considerable attention since the start of the genomics revolution. New technologies that have the potential to produce a step change in our understanding of the regulation of secondary metabolism are also described

Facilitating Scholarly Writing in Academic Medicine: Lessons Learned from a Collaborative Peer Mentoring Program

Scholarly writing is a critical skill for faculty in academic medicine; however, few faculty receive instruction in the process. We describe the experience of 18 assistant professors who participated in a writing and faculty development program which consisted of 7 monthly 75-minute sessions embedded in a Collaborative Mentoring Program (CMP). Participants identified barriers to writing, developed personal writing strategies, had time to write, and completed monthly writing contracts. Participants provided written responses to open-ended questions about the learning experience, and at the end of the program, participants identified manuscripts submitted for publication, and completed an audiotaped interview. Analysis of qualitative data using data reduction, data display, and conclusion drawing/verification showed that this writing program facilitated the knowledge, skills, and support needed to foster writing productivity. All participants completed at least 1 scholarly manuscript by the end of the CMP. The impact on participants’ future academic productivity requires long-term follow-up

Nutritional, structural and chemical defenses of common algae species against juvenile sea urchins

Este artículo contiene 14 páginas, 6 figuras, 3 tablas.Herbivory is a widespread biotic interaction with important ecological and evolutionary implications. Benthic marine systems show greater producer consumption than any other aquatic or terrestrial environment. Marine algae and plants have a variety of defensive mechanisms such as structural, chemical, and nutritional traits with the capacity to reduce herbivore consumption. These mechanisms can function simultaneously. Here, we quantified consumption by juvenile Diadema africanum and Paracentrotus lividus on 15 algal species (1) to investigate the relative contribution of algal nutritional, chemical, and structural traits to the patterns of consumption and (2) to assess whether this relative contribution varies as a function of herbivore species. Differences in consumption were found between sea urchins; however, changes differed across algal and herbivore species.There was no clear relationship between the nutritional contents and consumption rates on the studied species of algae. The structure and chemical defenses of algae species played an important role in the feeding behavior of the studied herbivores. Our results suggest that multiple defensive traits may be necessary to deter herbivores in the field.This study was funded by the ‘Fundación Caja Canarias’ under postgraduate fellowship (awarded to Adriana Rodríguez). This research is a contribution of the Consolidated Research Group "Grupo de Ecología Bentónica" (SGR2009-655) of the Catalan Government.Peer reviewe