MAJORA: Continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance

Genomic epidemiology has become an increasingly common tool for epidemic response. Recent technological advances have made it possible to sequence genomes rapidly enough to inform outbreak response, and cheaply enough to justify dense sampling of even large epidemics. With increased availability of sequencing it is possible for agile networks of sequencing facilities to collaborate on the sequencing and analysis of epidemic genomic data. In response to the ongoing SARS-CoV-2 pandemic in the United Kingdom, the COVID-19 Genomics UK (COG-UK) consortium was formed with the aim of rapidly sequencing SARS-CoV-2 genomes as part of a national-scale genomic surveillance strategy. The network consists of universities, academic institutes, regional sequencing centres and the four UK Public Health Agencies. We describe the development and deployment of Majora, an encompassing digital infrastructure to address the challenge of collecting and integrating both genomic sequencing data and sample-associated metadata produced across the COG-UK network. The system was designed and implemented pragmatically to stand up capacity rapidly in a pandemic caused by a novel virus. This approach has underpinned the success of COG-UK, which has rapidly become the leading contributor of SARS-CoV-2 genomes to international databases and has generated over 60,000 sequences to date.

Impact of Pretransplantation (18)F-Fluorodeoxyglucose-Positron Emission Tomography on Survival Outcomes after T Cell-Depleted Allogeneic Transplantation for Hodgkin Lymphoma.

Pretransplant (18)F-fluorodeoxyglucose (FDG) positron emission tomography status is an important prognostic factor for outcomes after autologous stem cell transplantation (SCT) in Hodgkin lymphoma (HL), but its impact on outcomes after allogeneic SCT remains unclear. We retrospectively evaluated outcomes after T cell-depleted allogeneic SCT of 116 patients with nonprogressive HL according to pretransplant Deauville scores. Endpoints were overall survival (OS), progression-free survival (PFS), relapse rate (RR), and nonrelapse-related mortality (NRM). OS, PFS, and RR did not differ significantly between the Deauville 1 to 2 and Deauville 3 to 5 cohorts (OS: 77.5% versus 67.3%, P = .49; PFS: 59.4% versus 55.7%, P = .43; RR: 20.9% versus 22.6%, P = .28 at 4 years). Differences in PFS remained statistically nonsignificant when comparisons were made between Deauville 1 to 3 and Deauville 4 to 5 cohorts (60.9% versus 51.4%, P = .10), and RR remained very similar (21.5% versus 23.8%, P = .42). Multivariate analyses demonstrated trends toward significance for an effect of Deauville score on PFS (hazard ratio 1.82 for Deauville 4 to 5, P = .06) and for number of lines of prior therapy on OS (hazard ratio 2.34 for >5 lines, P = .10). The latter effect appeared to be driven by higher NRM rather than increased RR. Our findings suggest that Deauville score before allogeneic SCT in patients with nonprogressive HL has a relatively modest impact on survival outcomes in comparison with the impact in autologous SCT and that predictive values for the individual patient remain low, indicating that residual FDG-avid disease should not preclude allogeneic SCT. Furthermore, our findings bring into question the importance of attainment of metabolic complete response in this setting if it is at the expense of increasing NRM risk.

Photoemission, resonant photoemission, and x-ray absorption of a Ru(II) complex adsorbed on rutile TiO2(110) prepared by in situ electrospray deposition.

An experimental study of the bonding geometry and electronic coupling of cis-bis(isothiocyanato)bis(2,2(')-bipyridyl-4,4(')-dicarboxylato)-ruthenium(II) (N3) adsorbed on rutile TiO(2)(110) is presented, along with supporting theoretical calculations of the bonding geometry. Samples were prepared in situ using ultrahigh vacuum electrospray deposition. Core-level photoemission spectroscopy was used to characterize the system and to deduce the nature of the molecule-surface bonding. Valence band photoemission and N 1s x-ray absorption spectra were aligned in a common binding energy scale to enable a quantitative analysis of the bandgap region. A consideration of the energetics in relation to optical absorption is used to identify the photoexcitation channel between the highest occupied and lowest unoccupied molecular orbitals in this system, and also to quantify the relative binding energies of core and valence excitons. The core-hole clock implementation of resonant photoemission spectroscopy is used to reveal that electron delocalization from N3 occurs within 16 fs.

Lip biting in a patient with Chiari type II malformation: case report.

Self mutilation of lips and tongue is considered a common type of Self-Injurious Behavior (SIB). Treatment of SIB in the form of Lip-Biting in developmentally disabled individuals has been the focus of several related reports using different oral appliances preventing or inhibiting the SIB. In this paper we report a case of SIB in the form of Lip-Biting on an infant with Chiari Type II Malformation which was treated with a Lip-bumper. The Lip-bumper demonstrated to be a viable option in treating transient and acute episodes of SIB involving the lower lip and buccal mucosa.