Efficient Reconciliation of Genomic Datasets of High Similarity

We apply Invertible Bloom Lookup Tables (IBLTs) to the comparison of k-mer sets originated from large DNA sequence datasets. We show that for similar datasets, IBLTs provide a more space-efficient and, at the same time, more accurate method for estimating Jaccard similarity of underlying k-mer sets, compared to MinHash which is a go-to sketching technique for efficient pairwise similarity estimation. This is achieved by combining IBLTs with k-mer sampling based on syncmers, which constitute a context-independent alternative to minimizers and provide an unbiased estimator of Jaccard similarity. A key property of our method is that involved data structures require space proportional to the difference of k-mer sets and are independent of the size of sets themselves. As another application, we show how our ideas can be applied in order to efficiently compute (an approximation of) k-mers that differ between two datasets, still using space only proportional to their number. We experimentally illustrate our results on both simulated and real data (SARS-CoV-2 and Streptococcus Pneumoniae genomes). © Yoshihiro Shibuya, Djamal Belazzougui, and Gregory Kucherov.

COVID-19 transmission in dental and oral/maxillofacial surgical practice during pandemic: questionnaire survey in 51 university hospitals in Japan.

BACKGROUND: The coronavirus disease 2019 (COVID-19) pandemic has become a major public health problem. Dental procedures that generate aerosols are considered to impose a high risk of infection; therefore, dental professionals, such as dentists and dental hygienists, may be at high risk of viral transmission. However, few studies have reported COVID-19 clusters in dental care settings. AIM: To investigate whether dental and oral/maxillofacial procedures are associated with the occurrence of COVID-19 clusters and measures taken to prevent nosocomial infection in dental clinics. METHODS: An online questionnaire survey on clinical activities (administrative control), infection control measures (environmental/engineering control, personal protective equipment, etc.), and confirmed or probable COVID-19 cases among patients and clinical staff was administered to the faculties of the dental and oral/maxillofacial surgical departments of university hospitals. FINDINGS: Fifty-one faculty members completed the questionnaire. All members were engaged in the treatment of dental and oral surgical outpatients and actively implemented standard precautions. Fourteen faculty members treated patients with COVID-19, but no infections transmitted from the patients to the medical staff were observed. In seven facilities, patients were found to have the infection after treatment (medical staff came in close contact), but there was no transmission from patients to medical staff. Four facilities had medical staff with infections, but none of them exhibited disease transmission from staff to patients. CONCLUSION: COVID-19 clusters are unlikely to occur in dental and oral surgical care settings if appropriate protective measures are implemented.

An Influence of User's Avatar Display on Conversation in Web Conferencing

Due to the COVID-19 epidemic, the use of web conferencing systems has become widespread but many people are not likely to send their own camera images. Muting the camera is usable to hide a participant but other participants can not aware the hided participant's non-verbal information. The purpose of this study is to investigate how the ease of conversation is affected when the participants are displayed as avatars instead of actual images in a web conferencing system. For the purpose, we investigated whether the fidelity of participant's image influence on the ease of conversation experimentally. We used four kinds of participant's image, they were default still image, avatar image, point image, and real image. Experimental result showed the possibility that the avatar facial image reduced the participant's embarrassment. Some participants felt that the system using avatar or point image improved the ease of conversation compared to the system using default non-moving image or real image. © 2021 IEEE.

Multisystem Inflammatory Syndrome in Children (MIS-C) with COVID-19: Insights from simultaneous familial Kawasaki Disease cases.

Recently, an increasing number of SARS-CoV-2 patients with COVID-19 syndrome, which overlaps with Kawasaki Disease (KD), have been reported, supporting the suggestion that infection is one of the triggers of KD. We summarized the reports of simultaneous familial KD cases to better understand the etiopathogenesis of both KD and Multisystem Inflammatory Syndrome in Children (MIS-C) related to COVID-19. Here we discuss the etiology of these syndromes from the point of view of infection and genetic susceptibility.