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Strategies for assembling large, complex genomes have evolved to include a combination of whole-genome shotgun sequencing and hierarchal map-assisted sequencing 1 , 2 . Whole-genome maps of all types can aid genome assemblies, generally starting with low-resolution cytogenetic maps and ending with the highest resolution of sequence. Fingerprint clone maps are based upon complete restriction enzyme digests of clones representative of the target genome, and ultimately comprise a near-contiguous path of clones across the genome. Such clone-based maps are used to validate sequence assembly order, supply long-range linking information for assembled sequences, anchor sequences to the genetic map and provide templates for closing gaps. Fingerprint maps are also a critical resource for subsequent functional genomic studies, because they provide a redundant and ordered sampling of the genome with clones 3 . In an accompanying paper 4 we describe the draft genome sequence of the chicken, Gallus gallus , the first species sequenced that is both a model organism and a global food source. Here we present a clone-based physical map of the chicken genome at 20-fold coverage, containing 260 contigs of overlapping clones. This map represents approximately 91% of the chicken genome and enables identification of chicken clones aligned to positions in other sequenced genomes.

This paper describes the research protocol for a randomized controlled trial of a self-management intervention for adults diagnosed with sickle cell disease (SCD). People living with SCD experience lifelong recurrent episodes of acute and chronic pain, which are exacerbated by stress. This study aims to decrease stress and improve SCD pain control with reduced opioid use through an intervention with self-management relaxation exercises, named You Cope, We Support (YCWS). Building on our previous findings from formative studies, this study is designed to test the efficacy of YCWS on stress intensity, pain intensity, and opioid use in adults with SCD. A randomized controlled trial of the short-term (8 weeks) and long-term (6 months) effects of YCWS on stress, pain, and opioid use will be conducted with 170 adults with SCD. Patients will be randomized based on 1:1 ratio (stratified on pain intensity [≤5 or >5]) to be either in the experimental (self-monitoring of outcomes, alerts or reminders, and use of YCWS [relaxation and distraction exercises and support]) or control (self-monitoring of outcomes and alerts or reminders) group. Patients will be asked to report outcomes daily. During weeks 1 to 8, patients in both groups will receive system-generated alerts or reminders via phone call, text, or email to facilitate data entry (both groups) and intervention use support (experimental). If the participant does not enter data after 24 hours, the study support staff will contact them for data entry troubleshooting (both groups) and YCWS use (experimental). We will time stamp and track patients' web-based activities to understand the study context and conduct exit interviews on the acceptability of system-generated and staff support. This study was approved by our institutional review board. This study was funded by the National Institute of Nursing Research of the National Institutes of Health in 2020. The study began in March 2021 and will be completed in June 2025. As of April 2022, we have enrolled 45.9% (78/170) of patients. We will analyze the data using mixed effects regression models (short term and long term) to account for the repeated measurements over time and use machine learning to construct and evaluate prediction models. Owing to the COVID-19 pandemic, the study was modified to allow for mail-in consent process, internet-based consent process via email or Zoom videoconference, devices delivered by FedEx, and training via Zoom videoconference. We expect the intervention group to report reductions in pain intensity (primary outcome; 0-10 scale) and in stress intensity (0-10 scale) and opioid use (Wisepill event medication monitoring system), which are secondary outcomes. Our study will contribute to advancing the use of nonopioid therapy such as guided relaxation and distraction techniques for managing SCD pain. ClinicalTrials.gov NCT04484272; https://clinicaltrials.gov/ct2/show/NCT04484272. PRR1-10.2196/33818.

Antiretroviral therapy (ART) cannot cure HIV infection because of a persistent reservoir of latently infected cells. Approaches that force HIV transcription from these cells, making them susceptible to killing—termed kick and kill regimens—have been explored as a strategy towards an HIV cure. RIVER is the first randomised trial to determine the effect of ART-only versus ART plus kick and kill on markers of the HIV reservoir. This phase 2, open-label, multicentre, randomised, controlled trial was undertaken at six clinical sites in the UK. Patients aged 18–60 years who were confirmed as HIV-positive within a maximum of the past 6 months and started ART within 1 month from confirmed diagnosis were randomly assigned by a computer generated randomisation list to receive ART-only (control) or ART plus the histone deacetylase inhibitor vorinostat (the kick) and replication-deficient viral vector T-cell inducing vaccines encoding conserved HIV sequences ChAdV63. HIVconsv-prime and MVA.HIVconsv-boost (the kill; ART + V + V; intervention). The primary endpoint was total HIV DNA isolated from peripheral blood CD4+ T-cells at weeks 16 and 18 after randomisation. Analysis was by intention to treat. This trial is registered with ClinicalTrials.gov, NCT02336074. Between June 14, 2015 and Jul 11, 2017, 60 men with HIV were randomly assigned to receive either an ART-only (n=30) or an ART + V + V (n=30) regimen; all 60 participants completed the study, with no loss-to-follow-up. Mean total HIV DNA at weeks 16 and 18 after randomisation was 3·02 log10 copies HIV DNA per 106 CD4+ T-cells in the ART-only group versus 3·06 log10 copies HIV DNA per 106 CD4+ T-cells in ART + V + V group, with no statistically significant difference between the two groups (mean difference of 0·04 log10 copies HIV DNA per 106 CD4+ T-cells [95% CI −0·03 to 0·11; p=0·26]). There were no intervention-related serious adverse events. This kick and kill approach conferred no significant benefit compared with ART alone on measures of the HIV reservoir. Although this does not disprove the efficacy kick and kill strategy, for future trials enhancement of both kick and kill agents will be required. Medical Research Council (MR/L00528X/1).

SPHERE (Beuzit et al,. 2019) has now been in operation at the VLT for more than 5 years, demonstrating a high level of performance. SPHERE has produced outstanding results using a variety of operating modes, primarily in the field of direct imaging of exoplanetary systems, focusing on exoplanets as point sources and circumstellar disks as extended objects. The achievements obtained thus far with SPHERE (~200 refereed publications) in different areas (exoplanets, disks, solar system, stellar physics...) have motivated a large consortium to propose an even more ambitious set of science cases, and its corresponding technical implementation in the form of an upgrade. The SPHERE+ project capitalizes on the expertise and lessons learned from SPHERE to push high contrast imaging performance to its limits on the VLT 8m-telescope. The scientific program of SPHERE+ described in this document will open a new and compelling scientific window for the upcoming decade in strong synergy with ground-based facilities (VLT/I, ELT, ALMA, and SKA) and space missions (Gaia, JWST, PLATO and WFIRST). While SPHERE has sampled the outer parts of planetary systems beyond a few tens of AU, SPHERE+ will dig into the inner regions around stars to reveal and characterize by mean of spectroscopy the giant planet population down to the snow line. Building on SPHERE's scientific heritage and resounding success, SPHERE+ will be a dedicated survey instrument which will strengthen the leadership of ESO and the European community in the very competitive field of direct imaging of exoplanetary systems. With enhanced capabilities, it will enable an even broader diversity of science cases including the study of the solar system, the birth and death of stars and the exploration of the inner regions of active galactic nuclei.