G4RNA: an RNA G-quadruplex database

Abstract: G-quadruplexes (G4) are tetrahelical structures formed from planar arrangement of guanines in nucleic acids. A simple, regular motif was originally proposed to describe G4-forming sequences. More recently, however, formation of G4 was discovered to depend, at least in part, on the contextual backdrop of neighboring sequences. Prediction of G4 folding is thus becoming more challenging as G4 outlier structures, not described by the originally proposed motif, are increasingly reported. Recent observations thus call for a comprehensive tool, capable of consolidating the expanding information on tested G4s, in order to conduct systematic comparative analyses of G4-promoting sequences. The G4RNA Database we propose was designed to help meet the need for easily-retrievable data on known RNA G4s. A user-friendly, flexible query system allows for data retrieval on experimentally tested sequences, from many separate genes, to assess G4-folding potential. Query output sorts data according to sequence position, G4 likelihood, experimental outcomes and associated bibliographical references. G4RNA also provides an ideal foundation to collect and store additional sequence and experimental data, considering the growing interest G4s currently generate

Operationalizing COLREGs in SMART ship navigation

The maritime industry is undergoing a transformation driven by digitalization and connectivity. The technological realization of Maritime Autonomous Surface Ships (MASS) presents significant challenges for the maritime human factors research community. These challenges relate to system design, human-automation interaction, stakeholder training, use and acceptance of new technology systems, and on a larger scale, how the regulatory framework, including the Collision Regulations (COLREGs) will be impacted within a MASS system. Decision support is the next step in the transformation towards more connected ships, however, such systems for navigation are largely unexplored from the users’ perspective.The decision support system studied in this project was developed by W\ue4rtsil\ue4 and is called Advanced Intelligent Manoeuvring (AIM), aligning with “low-level automation” or Level 1 (out of a 4-level progression) of MASS. AIM can generate suggestions for course or speed alterations based on data from surrounding traffic. A full-mission bridge simulator study was conducted at Chalmers University of Technology in Gothenburg, Sweden with nineteen Swedish navigators. Three traffic scenarios each with three ships were completed in both baseline (no AIM) and AIM conditions. A mixed methods data collection and analysis approach was employed using questionnaires, collective interviews, and an evaluation of the ship tracks. The results show that the navigators perceive AIM as an advisory tool, to visualize how traffic situations could unfold, an outcome currently difficult for most navigators to conceive. This report discusses the present and near future of the maritime sociotechnical system, highlighting the benefits of automation, while remaining vigilant about the potential dangers

A scoping review of distributed ledger technology in genomics: thematic analysis and directions for future research

Objective Rising interests in distributed ledger technology (DLT) and genomics have sparked various interdisciplinary research streams with a proliferating number of scattered publications investigating the application of DLT in genomics. This review aims to uncover the current state of research on DLT in genomics, in terms of focal research themes and directions for future research. Materials and Methods We conducted a scoping review and thematic analysis. To identify the 60 relevant papers, we queried Scopus, Web of Science, PubMed, ACM Digital Library, IEEE Xplore, arXiv, and BiorXiv. Results Our analysis resulted in 7 focal themes on DLT in genomics discussed in literature, namely: (1) Data economy and sharing; (2) Data management; (3) Data protection; (4) Data storage; (5) Decentralized data analysis; (6) Proof of useful work; and (7) Ethical, legal, and social implications. Discussion Based on the identified themes, we present 7 future research directions: (1) Investigate opportunities for the application of DLT concepts other than Blockchain; (2) Explore people’s attitudes and behaviors regarding the commodification of genetic data through DLT-based genetic data markets; (3) Examine opportunities for joint consent management via DLT; (4) Investigate and evaluate data storage models appropriate for DLT; (5) Research the regulation-compliant use of DLT in healthcare information systems; (6) Investigate alternative consensus mechanisms based on Proof of Useful Work; and (7) Explore DLT-enabled approaches for the protection of genetic data ensuring user privacy. Conclusion While research on DLT in genomics is currently growing, there are many unresolved problems. This literature review outlines extant research and provides future directions for researchers and practitioners

Gamma and beta bursts during working memory readout suggest roles in its volitional control

Working memory (WM) activity is not as stationary or sustained as previously thought. There are brief bursts of gamma (~50-120 Hz) and beta (~20-35 Hz) oscillations, the former linked to stimulus information in spiking. We examined these dynamics in relation to readout and control mechanisms of WM. Monkeys held sequences of two objects in WM to match to subsequent sequences. Changes in beta and gamma bursting suggested their distinct roles. In anticipation of having to use an object for the match decision, there was an increase in gamma and spiking information about that object and reduced beta bursting. This readout signal was only seen before relevant test objects, and was related to premotor activity. When the objects were no longer needed, beta increased and gamma decreased together with object spiking information. Deviations from these dynamics predicted behavioral errors. Thus, beta could regulate gamma and the information in WM.National Institute of Mental Health (U.S.) (Grant R37MH087027)United States. Office of Naval Research (Grant N00014-16-1-2832

A scoping review of distributed ledger technology in genomics: thematic analysis and directions for future research

OBJECTIVE: Rising interests in distributed ledger technology (DLT) and genomics have sparked various interdisciplinary research streams with a proliferating number of scattered publications investigating the application of DLT in genomics. This review aims to uncover the current state of research on DLT in genomics, in terms of focal research themes and directions for future research. MATERIALS AND METHODS: We conducted a scoping review and thematic analysis. To identify the 60 relevant papers, we queried Scopus, Web of Science, PubMed, ACM Digital Library, IEEE Xplore, arXiv, and BiorXiv. RESULTS: Our analysis resulted in 7 focal themes on DLT in genomics discussed in literature, namely: (1) Data economy and sharing; (2) Data management; (3) Data protection; (4) Data storage; (5) Decentralized data analysis; (6) Proof of useful work; and (7) Ethical, legal, and social implications. DISCUSSION: Based on the identified themes, we present 7 future research directions: (1) Investigate opportunities for the application of DLT concepts other than Blockchain; (2) Explore people’s attitudes and behaviors regarding the commodification of genetic data through DLT-based genetic data markets; (3) Examine opportunities for joint consent management via DLT; (4) Investigate and evaluate data storage models appropriate for DLT; (5) Research the regulation-compliant use of DLT in healthcare information systems; (6) Investigate alternative consensus mechanisms based on Proof of Useful Work; and (7) Explore DLT-enabled approaches for the protection of genetic data ensuring user privacy. CONCLUSION: While research on DLT in genomics is currently growing, there are many unresolved problems. This literature review outlines extant research and provides future directions for researchers and practitioners

Efficacy and safety of ceftobiprole in patients aged 65 years or older:a post hoc analysis of three Phase III studies

Lay abstract Infections are a common cause of severe disease and death in older patients. Antibiotic treatment may also be complicated by age-related changes within the body. The present study analyzed results from three large clinical trials that assessed the benefits of the novel antibiotic ceftobiprole in the older population. In patients aged over 65 years with skin infections or with pneumonia acquired either in the community or in a hospital setting, ceftobiprole offered similar benefits to established antibiotics. There was also some preliminary evidence that older patients may respond more quickly to ceftobiprole compared with the other antibiotics used in these studies. Overall, ceftobiprole was well tolerated and will be a useful treatment option for infections in older patients. Aim: To evaluate the efficacy and safety of ceftobiprole in patients aged >= 65 years. Materials & methods: We conducted a post hoc analysis of three randomized, double-blind, Phase III studies in patients with acute bacterial skin and skin structure infections, community-acquired pneumonia and hospital-acquired pneumonia. Results: Findings for patients aged >= 65 years (n = 633) were consistent with those for the overall study populations, although a trend toward improved outcomes was reported in some subgroups, for example, patients aged >= 75 years with community-acquired pneumonia were more likely to achieve an early clinical response with ceftobiprole than comparator (treatment difference 16.3% [95% CI:1.8-30.8]). The safety profile was similar between treatment groups in all studies. Conclusion: This analysis further supports the efficacy and safety of ceftobiprole in older patients with acute bacterial skin and skin structure infections or pneumonia. Clinicaltrials.gov trial identifiers: , ,

Gamma and Beta Bursts Underlie Working Memory

Working memory is thought to result from sustained neuron spiking. However, computational models suggest complex dynamics with discrete oscillatory bursts. We analyzed local field potential (LFP) and spiking from the prefrontal cortex (PFC) of monkeys performing a working memory task. There were brief bursts of narrow-band gamma oscillations (45–100 Hz), varied in time and frequency, accompanying encoding and re-activation of sensory information. They appeared at a minority of recording sites associated with spiking reflecting the to-be-remembered items. Beta oscillations (20–35 Hz) also occurred in brief, variable bursts but reflected a default state interrupted by encoding and decoding. Only activity of neurons reflecting encoding/decoding correlated with changes in gamma burst rate. Thus, gamma bursts could gate access to, and prevent sensory interference with, working memory. This supports the hypothesis that working memory is manifested by discrete oscillatory dynamics and spiking, not sustained activity.National Institute of Mental Health (U.S.) (Grant 5R01MH091174-05)National Institute of Mental Health (U.S.) (Grant 5R37MH087027-07

A single H/ACA small nucleolar RNA mediates tumor suppression downstream of oncogenic RAS.

Small nucleolar RNAs (snoRNAs) are a diverse group of non-coding RNAs that direct chemical modifications at specific residues on other RNA molecules, primarily on ribosomal RNA (rRNA). SnoRNAs are altered in several cancers; however, their role in cell homeostasis as well as in cellular transformation remains poorly explored. Here, we show that specific subsets of snoRNAs are differentially regulated during the earliest cellular response to oncogenic RASG12V expression. We describe a novel function for one H/ACA snoRNA, SNORA24, which guides two pseudouridine modifications within the small ribosomal subunit, in RAS-induced senescence in vivo. We find that in mouse models, loss of Snora24 cooperates with RASG12V to promote the development of liver cancer that closely resembles human steatohepatitic hepatocellular carcinoma (HCC). From a clinical perspective, we further show that human HCCs with low SNORA24 expression display increased lipid content and are associated with poor patient survival. We next asked whether ribosomes lacking SNORA24-guided pseudouridine modifications on 18S rRNA have alterations in their biophysical properties. Single-molecule Fluorescence Resonance Energy Transfer (FRET) analyses revealed that these ribosomes exhibit perturbations in aminoacyl-transfer RNA (aa-tRNA) selection and altered pre-translocation ribosome complex dynamics. Furthermore, we find that HCC cells lacking SNORA24-guided pseudouridine modifications have increased translational miscoding and stop codon readthrough frequencies. These findings highlight a role for specific snoRNAs in safeguarding against oncogenic insult and demonstrate a functional link between H/ACA snoRNAs regulated by RAS and the biophysical properties of ribosomes in cancer