Improving the time and space complexity of the WFA algorithm and generalizing its scoring

Modern genomic sequencing data is trending toward longer sequences with higher accuracy. Many analyses using these data will center on alignments, but classical exact alignment algorithms are infeasible for long sequences. The recently proposed WFA algorithm demonstrated how to perform exact alignment for long, similar sequences in O(sN) time and O(s2) memory, where s is a score that is low for similar sequences (Marco-Sola et al., 2021). However, this algorithm still has infeasible memory requirements for longer sequences. Also, it uses an alternate scoring system that is unfamiliar to many bioinformaticians. We describe variants of WFA that improve its asymptotic memory use from O(s2) to O(s3/2) and its asymptotic run time from O(sN) to O(s2 + N). We expect the reduction in memory use to be particularly impactful, as it makes it practical to perform highly multithreaded megabase-scale exact alignments in common compute environments. In addition, we show how to fold WFA's alternate scoring into the broader literature on alignment scores.

Investigating the Use of Head Mounted Devices for Remote Cooperation and Guidance during the Treatment of Wounds

Professional caregivers often face complex situations in which they need the support of a colleague or a specialist. This is especially necessary for caregivers during their training or with less practice in certain tasks. Due to time and space restrictions, colleagues or specialists are not always available for local support. Remote support by streaming videos to a remote helper has been discussed in healthcare domains as a so-called teleconsultation. However, little is known about how to apply teleconsultation in care. We conducted a study with caregivers and remote helpers to compare head mounted devices (HMDs) for teleconsultation in care to two alternative solutions using smartphones. We found that despite lacking familiarity, HMDs have good potential for remote support in care, and that creating video streams with smartphones is not preferable for teleconsultations. We suggest that ideal support needs to balance freedom and guidance and suggest how such support needs to be further explored.

Konceptuelle metaforer som selektionskriterium for Dansk litteraturs kanon - med fokus på elevers literacytilegnelse på tværs af tidsrum, sprog og kultur i arbejdet med kanonlitteratur

This article argues that an increased focus on the inherent conceptual metaphors of chronotopes in canonical literature may contribute to students’ awareness of the historical and literary development in time and space. Thus, expanding their literacy-skills acquisition in comparison to the linear chronological periodization, author-portrait and text reading that typically characterize the reading of canon literature. Furthermore, the article argues that an increased focus on bi- and multilingual students’ interpretation of conceptual metaphors may contribute to the historical and literary development.

Microbial ecosystems as targets for improving pig gut health

To date, our understanding of the organisms which constitute the microbiomes of humans and our domesticated species has been limited by the technologies available to study them. Progress from culture to species-based DNA approaches has allowed us to appreciate the scale of animal microbiomes and the changes which can occur over time and space. However, in order to design and validate rational approaches to manipulating microbiomes to optimise health, welfare and productivity, we need to begin to understand them as ecosystems, in which the host and a complex mixture of micro-organisms are continuously engaged both in co-operation to produce resources from food and in competition for those resources. The application of ecological principles can guide this understanding, but we need to validate the concepts we use, since they may not all be as applicable as they might seem.