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Background: Locally recurrent rectal cancer (LRRC) occurs in 5-10% of patients following previous treatment of rectal cancer. It has a significant impact on patients' overall health-related quality of life (HrQoL). Major advances in surgical treatments have led to improved survival outcomes. However, due to the lack of disease-specific, validated patient-reported outcome measure (PROM), HrQoL, is variably assessed. The aim of this study is to develop a disease-specific, psychometrically robust, and validated PROM for use in LRRC., Methods: A multicentre, three phase, mixed-methods, observational study was performed across five centres in the UK and Australia. Adult patients (>18 years old) with an existing or previously treated LRRC within the last 2 years were eligible to participate. Patients completed the proposed LRRC-QoL, EORTC QLQ-CR29, and FACT-C questionnaires. Scale structure was analysed using multi-trait scaling analysis and exploratory factor analysis, reliability was assessed using Cronbach's and the intra-class coefficient, convergent validity was assessed using Pearson's correlation, and known-groups comparison was assessed using the student t-test or ANOVA., Findings: Between 01/03/2015 and 31/12/2019, 117 patients with a diagnosis of LRRC were recruited. The final scale structure of the LRRC-QoL consisted of nine multi-item scales (healthcare services, psychological impact, pain, urostomy-related symptoms, lower limb symptoms, stoma, sexual function, sexual interest, and urinary symptoms) and three single items. Cronbach's Alpha and Intraclass correlation values of >0.7 across the majority of scales supported overall reliability. Convergent validity was demonstrated between LRRC-QoL Pain Scale and FACT-C Physical Well Being scale (r = 0.528, p < 0.001), LRRC-QoL Psychological Impact scale with EORTC QLQ CR29 Body Image (r = 0.680, p < 0.001) and the FACT-C Emotional Well Being scale (r = 0.326, p < 0.001), and LRRC-QoL Urinary Symptoms scale with EORTC QLQ-CR29 Urinary Frequency scale (r = 0.310, p < 0.001). Known-groups validity was demonstrated for gender, disease location, treatment intent, and re-recurrent disease., Interpretation: The LRRC-QoL has demonstrated robust psychometric properties and can be used in clinical and academic practice., Funding: None., Competing Interests: GV has received consulting fees from Pfizer, Eisa and Roche. She has received honoraria from Novartis, AstraZeneca and Pfizer. She sits on advisory boards for Sanofi and Seattle Genetics. The other authors have no declared conflicts of interest. NM is undertaking a PhD funded by from Bowel and Cancer Research UK., (© 2023 The Authors.)

Background: The approval of Bruton tyrosine kinase (BTK) inhibitors in patients with previously untreated chronic lymphocytic leukaemia (CLL) was based on trials which compared ibrutinib with alkylating agents in patients considered unfit for fludarabine, cyclophosphamide, and rituximab, the most effective chemoimmunotherapy in CLL. We aimed to assess whether ibrutinib and rituximab is superior to fludarabine, cyclophosphamide, and rituximab in terms of progression-free survival., Methods: This study is an interim analysis of FLAIR, which is an open-label, randomised, controlled, phase 3 trial in patients with previously untreated CLL done at 101 UK National Health Service hospitals. Eligible patients were between 18 and 75 years of age with a WHO performance status of 2 or less and disease status requiring treatment according to International Workshop on CLL criteria. Patients with greater than 20% of their CLL cells having the chromosome 17p deletion were excluded. Patients were randomly assigned (1:1) by means of minimisation (Binet stage, age, sex, and centre) with a random element in a web-based system to ibrutinib and rituximab (ibrutinib administered orally at 420 mg/day for up to 6 years; rituximab administered intravenously at 375 mg/m 2 on day 1 of cycle 1 and at 500 mg/m 2 on day 1 of cycles 2-6 of a 28-day cycle) or fludarabine, cyclophosphamide, and rituximab (fludarabine 24 mg/m 2 per day orally on day 1-5, cyclophosphamide 150 mg/m 2 per day orally on days 1-5; rituximab as above for up to 6 cycles). The primary endpoint was progression-free survival, analysed by intention to treat. Safety analysis was per protocol. This study is registered with ISRCTN, ISRCTN01844152, and EudraCT, 2013-001944-76, and recruiting is complete., Findings: Between Sept 19, 2014, and July 19, 2018, of 1924 patients assessed for eligibility, 771 were randomly assigned with median age 62 years (IQR 56-67), 565 (73%) were male, 206 (27%) were female and 507 (66%) had a WHO performance status of 0. 385 patients were assigned to fludarabine, cyclophosphamide, and rituximab and 386 patients to ibrutinib and rituximab. After a median follow-up of 53 months (IQR 41-61) and at prespecified interim analysis, median progression-free survival was not reached (NR) with ibrutinib and rituximab and was 67 months (95% CI 63-NR) with fludarabine, cyclophosphamide, and rituximab (hazard ratio 0·44 [95% CI 0·32-0·60]; p<0·0001). The most common grade 3 or 4 adverse event was leukopenia (203 [54%] patients in the fludarabine, cyclophosphamide, and rituximab group and 55 [14%] patients in the ibrutinib and rituximab group. Serious adverse events were reported in 205 (53%) of 384 patients receiving ibrutinib and rituximab compared with 203 (54%) of 378 patients receiving fludarabine, cyclophosphamide, and rituximab. Two deaths in the fludarabine, cyclophosphamide, and rituximab group and three deaths in the ibrutinib and rituximab group were deemed to be probably related to treatment. There were eight sudden unexplained or cardiac deaths in the ibrutinib and rituximab group and two in the fludarabine, cyclophosphamide, and rituximab group., Interpretation: Front line treatment with ibrutinib and rituximab significantly improved progression-free survival compared with fludarabine, cyclophosphamide, and rituximab but did not improve overall survival. A small number of sudden unexplained or cardiac deaths in the ibrutinib and rituximab group were observed largely among patients with existing hypertension or history of cardiac disorder., Funding: Cancer Research UK and Janssen., Competing Interests: Declaration of interests PH reports funding for the study and provision of investigational medicinal products from Janssen and AbbVie; personal consulting fees from Janssen, AbbVie, and AstraZeneca; personal speaker fees from Janssen, AbbVie, AstraZeneca, and BeiGene; institutional support of clinical trials from Janssen, AbbVie, Gilead Sciences, and F Hoffman-La Roche. AP reports unrestricted educational grants to her institution from Janssen, Pharmacyclics, and AbbVie. ABl reports speaker fees from Janssen and AbbVie and support for conference attendance from AbbVie. ABr reports personal payment for presentations from Janssen-Cilag and AstraZeneca and personal payment for attending meetings from AbbVie. BK reports personal payment or honoraria for lectures from AbbVie and AstraZeneca and a voluntary unpaid role as CLL Support Associate Trustee. RW reports payment for lectures from AbbVie, AstraZeneca, Janssen, and BeiGene; support for attending meetings from AbbVie and Janssen; and participation on a data safety monitoring board or advisory board for AstraZeneca, Janssen, SecuraBio, and AbbVie. MF reports travel support for conference attendance from AbbVie and remunerated participation on an advisory board for AstraZeneca. GP reports honoraria for delivering educational sessions from Janssen-Cilag and Roche. NM reports payment or honoraria for presentations from Amgen and Kite Gilead; support for attending meetings or travel from Takeda; and participation on a data safety monitoring board or advisory board for Kite Gilead, Amgen, and AbbVie. KC reports personal speakers fees from Roche, Takeda, Kite, Gilead, and Incyte; support for travel and registration for meetings from Roche, Takeda, Kite, and BMS; and participation on a data safety monitoring board or advisory board for Roche, Takeda, Celgene, Atara, Gilead, Kite, Janssen, and Incyte. AS reports receipt of part of her salary from the Oxford Biomedical Research Centre; grants from Janssen and AstraZeneca; honoraria for presentations from Roche, AbbVie, Janssen, BeiGene, and AstraZeneca; and receipt of equipment, materials, drugs, medical writing, gifts, or other services from Illumina, Oxford Nanopore Technology, and Adaptive Biotechnology. FF reports grants from Cancer Research UK and AbbVie; consulting fees from BC Platform; payment or honoraria for presentations from AbbVie, Janssen-Cilag, Acerta, and BeiGene; support for attending meetings or travel from AbbVie; and participation on a data safety monitoring board or advisory board for BeiGene. NE reports personal speaker payments from AstraZeneca and Roche and support for attending meetings and travel from AbbVie. SP reports personal honoraria for presentations from Gilead, AstraZeneca, AbbVie, BeiGene, and Takeda. CPF reports personal consultancy fees from AbbVie, AstraZeneca, Atarabio, BMS, GenMab, Gilead–Kite, Incyte, Lilly, Morphosys, Ono, Roche, and Takeda; payment for educational events from Janssen, Incyte, and Roche; institution research funding from BeiGene; support for attending meetings or travel from Roche; and participation on trial steering committees for GenMab, Morphosys, and Roche. DRH is employed by Roche and holds stock or stock options from Roche. AH reports unrestricted educational grants to her institution from Janssen, Pharmacyclics, and AbbVie and receipt of a speaker fee from AbbVie. JMB reports unrestricted educational grants to her institution from Janssen, Pharmacyclics, and AbbVie. DAC reports unrestricted educational grants to his institution from Janssen, Pharmacyclics, and AbbVie; payment to institution for educational lectures from Janssen; participation on a data safety monitoring board for an academically led investigator-initiated CLL study and personal payment for meeting attendance and report preparation from University Hospital Cologne. SJ reports receipt of unrestricted educational grants to her institution from Janssen, Pharmacyclics and AbbVie. NG reports unrestricted educational grants to her institution from Janssen, Pharmacyclics, and AbbVie and participation on an advisory board for AbbVie. PEMP reports grants from Roche and Gilead; payment or honoraria for presentations from AbbVie, AstraZeneca, BeiGene, Gilead, and Janssen; support for attending meetings or travel from AbbVie; and participation on a data safety monitoring board or advisory board for AbbVie, BeiGene, and Novartis. DA reports receipt of part of his salary from the National Institute for Health and Care Research and Medical Research Council and support to attend meetings from CSL Behring. AR reports grants to his institution from AbbVie, Janssen, Pharmacyclics, and Roche; consulting fees from BeiGene and Pharmacyclics paid to a company of which AR is a director; payment or honoraria for presentations from AbbVie, Beckman Coulter, BD Biosciences, BeiGene, and Janssen paid to a company of which AR is a director; support for attending meetings or travel from Janssen; participation on a data safety monitoring board or advisory board from AbbVie and Janssen; and receipt of equipment from Beckman Coulter. TM reports payment for lectures and presentations from Janssen, AbbVie, and AstraZeneca; support for attending conferences from Janssen, AbbVie, and AstraZeneca; and participation on advisory boards for Janssen, AbbVie, AstraZeneca, Lilly, BeiGene, and Morphosys. All other authors declare no competing interests., (Copyright © 2023 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license. Published by Elsevier Ltd.. All rights reserved.)

Background: Overall survival rates for locally recurrent rectal cancer (LRRC) continue to improve but the evidence concerning health-related quality of life (HrQoL) remains limited. The aim of this study was to describe the short-term HrQoL differences between patients undergoing surgical and palliative treatments for LRRC., Methods: An international, cross-sectional, observational study was undertaken at five centres across the UK and Australia. HrQoL in LRRC patients was assessed using the European Organisation for Research and Treatment of Cancer (EORTC) QLQ-CR29 and functional assessment of cancer therapy - colorectal (FACT-C) questionnaires and subgroups (curative versus palliative) were compared. Secondary analyses included the comparison of HrQoL according to the margin status, location of disease and type of treatment. Scores were interpreted using minimal clinically important differences (MCID) and Cohen effect size (ES)., Results: Out of 350 eligible patients, a total of 95 patients participated, 74.0 (78.0 per cent) treated with curative intent and 21.0 (22.0 per cent) with palliative intent. Median time between LRRC diagnosis and HrQoL assessments was 4 months. Higher overall FACT-C scores denoting better HrQoL were observed in patients undergoing curative treatment, demonstrating a MCID with a mean difference of 18.5 (P < 0.001) and an ES of 0.6. Patients undergoing surgery had higher scores denoting a higher burden of symptoms for the EORTC CR29 domains of urinary frequency (P < 0.001, ES 0.3) and frequency of defaecation (P < 0.001, ES 0.4). Higher overall FACT-C scores were observed in patients who underwent an R0 resection versus an R1 resection (P = 0.051, ES 0.6). EORTC CR29 scores identified worse body image in patients with posterior/central disease (P = 0.021). Patients undergoing palliative chemoradiation reported worse HrQoL scores with a higher symptom burden on the frequency of defaecation scale compared with palliative chemotherapy (P = 0.041)., Conclusion: Several differences in short-term HrQoL outcomes between patients undergoing curative and palliative treatment for LRRC were documented. Patients undergoing curative surgery reported better overall HrQoL and a higher burden of pelvic symptoms., (© The Author(s) 2023. Published by Oxford University Press on behalf of BJS Society Ltd.)

Friedreich's ataxia is an incurable disease caused by frataxin (FXN) protein deficiency, which is mostly induced by GAA repeat expansion in intron 1 of the FXN gene. Here, we identified antisense oligonucleotides (ASOs), complementary to two regions within the first intron of FXN pre-mRNA, which could increase FXN mRNA by ∼2-fold in patient fibroblasts. The increase in FXN mRNA was confirmed by the identification of multiple overlapping FXN-activating ASOs at each region, two independent RNA quantification assays, and normalization by multiple housekeeping genes. Experiments on cells with the ASO-binding sites deleted indicate that the ASO-induced FXN activation was driven by indirect effects. RNA sequencing analyses showed that the two ASOs induced similar transcriptome-wide changes, which did not resemble the transcriptome of wild-type cells. This RNA-seq analysis did not identify directly base-paired off-target genes shared across ASOs. Mismatch studies identified two guanosine-rich motifs (CCGG and G4) within the ASOs that were required for FXN activation. The phosphorodiamidate morpholino oligomer analogs of our ASOs did not activate FXN, pointing to a PS-backbone-mediated effect. Our study demonstrates the importance of multiple, detailed control experiments and target validation in oligonucleotide studies employing novel mechanisms such as gene activation., (© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Background: Medical technologies have the potential to improve quality and efficiency of healthcare. The design of clinical trials should consider participants' perspectives to optimise enrolment, engagement and satisfaction. This study aims to assess patients' perceptions of their involvement in medical device trials, to inform the designs of future medical technology implementation and evaluation., Methods: Four focus groups were undertaken with a total of 16 participants who had participated in a study testing hospital inpatient remote monitoring devices. Interviews were audio-recorded, transcribed verbatim and underwent thematic analysis., Results: Four main themes emerged: patients' motivations for participating in medical device research; patients' perceptions of technology in medicine; patients' understanding of trial methodology; and patients' perceptions of the benefits of involvement in medical device trials. The appeal of new technology is a contributing factor to the decision to consent, although concerns remain regarding risks associated with technology in healthcare settings. Perceived benefits of participating in device trials include extra care, social benefits and comradery with other participants seen using the devices, although there is a perceived lack of confidence in using technology amongst older patients., Conclusion: Future device trials should prioritise information sharing with participants both before and after the trial. Verbal and written information alongside practical demonstrations can help to combat a lack of confidence with technology. Randomised trials and those with placebo- or sham-controlled arms should not be considered as barriers to participation. Study results should be disseminated to participants in lay format as soon as possible, subject to participant permission.

The ocean-atmosphere exchange of CO 2 largely depends on the balance between marine microbial photosynthesis and respiration. Despite vast taxonomic and metabolic diversity among marine planktonic bacteria and archaea (prokaryoplankton) 1-3 , their respiration usually is measured in bulk and treated as a 'black box' in global biogeochemical models 4 ; this limits the mechanistic understanding of the global carbon cycle. Here, using a technology for integrated phenotype analyses and genomic sequencing of individual microbial cells, we show that cell-specific respiration rates differ by more than 1,000× among prokaryoplankton genera. The majority of respiration was found to be performed by minority members of prokaryoplankton (including the Roseobacter cluster), whereas cells of the most prevalent lineages (including Pelagibacter and SAR86) had extremely low respiration rates. The decoupling of respiration rates from abundance among lineages, elevated counts of proteorhodopsin transcripts in Pelagibacter and SAR86 cells and elevated respiration of SAR86 at night indicate that proteorhodopsin-based phototrophy 3,5-7 probably constitutes an important source of energy to prokaryoplankton and may increase growth efficiency. These findings suggest that the dependence of prokaryoplankton on respiration and remineralization of phytoplankton-derived organic carbon into CO 2 for its energy demands and growth may be lower than commonly assumed and variable among lineages., (© 2022. The Author(s).)

Background: Undertaking randomized clinical trials (RCTs) in emergency surgical settings is associated with methodological and practical challenges. This study explored patients' and clinicians' perspectives associated with the conduct of an RCT comparing laparoscopic and open colorectal surgery in the acute setting., Methods: All eligible patients screened and enrolled for the 'Laparoscopic versus open colorectal surgery in the acute setting (LaCeS)' multicentre, randomized clinical feasibility trial in five UK NHS Trusts were invited to respond to a survey. Patients and healthcare professionals were also invited to take part in semi-structured interviews. Survey and interviews explored the acceptability of the feasibility trial. Interviews were audio recorded, transcribed verbatim, and analysed using thematic analysis. Survey data were analysed descriptively to assess patient views of the trial and intervention., Results: Out of 72 patients enrolled for the LaCeS RCT, survey data were collected from 28 patients (38.9 per cent), and interviews were conducted with 16 patients and 14 healthcare professionals. Thirteen out of 28 patients (46 per cent) had treatment preferences but these were not strong enough to deter participation. Twelve of the patients interviewed believed that their surgeon preferred laparoscopic surgery, but this did not deter them from participating in the trial. Half of the surgeons interviewed expressed the view that laparoscopic surgery was of benefit in this setting, but recognized that the need for research evidence outweighed their personal treatment preferences. Eight of the 14 recruiters reported that the emergency setting affected recruitment, especially in centres with fewer recruiting surgeons. Interviewees reported that recruitment was helped significantly by using surgical trainees to consent patients., Conclusion: This study identified specific challenges for the LaCeS trial design to address and adds significant insights to our understanding of recruiting to emergency surgical trials more broadly., (© The Author(s) 2022. Published by Oxford University Press on behalf of BJS Society Ltd.)

The Myeloma X trial provided a platform to explore genetics in relation to systematic assessment of patient-reported outcomes at key points during salvage treatment in multiple myeloma (MM) patients. Blood DNA was obtained in 191 subjects for single nucleotide polymorphism (SNP) genotyping. By univariable analysis, the non-coding rs2562456 SNP, upstream of LINC00664, was associated with several relevant pain and health-related quality-of-life (HRQoL) scores at 100 days after allocation to consolidation with autologous stem cell transplantation or weekly cyclophosphamide. Presence of the minor (C) allele was associated with lower pain interference (p = 0.014) and HRQoL pain (p = 0.003), and higher HRQoL global health status (p = 0.011) and physical functioning (p = 0.007). These effects were not modified by treatment arm and were no longer significant at 6 months. Following induction therapy, the rs13361160 SNP near the CCT5 and FAM173B genes was associated with higher global health (p = 0.027) and physical functioning (p = 0.013). This exploratory study supports associations between subjective parameters in MM with SNPs previously identified in genome-wide association studies of pain. Conversely, SNPs in candidate genes involved in opioid and transporter pathways showed no effect. Further studies are warranted in well-defined cancer populations, and potentially assisted by whole genome sequencing with germline analysis in routine diagnostics in haematological cancers., (© 2022. The Author(s).)

The lung is a complex organ with various cell types having distinct roles. Antisense oligonucleotides (ASOs) have been studied in the lung, but it has been challenging to determine their effectiveness in each cell type due to the lack of appropriate analytical methods. We employed three distinct approaches to study silencing efficacy within different cell types. First, we used lineage markers to identify cell types in flow cytometry, and simultaneously measured ASO-induced silencing of cell-surface proteins CD47 or CD98. Second, we applied single-cell RNA sequencing (scRNA-seq) to measure silencing efficacy in distinct cell types; to the best of our knowledge, this is the first time scRNA-seq has been applied to measure the efficacy of oligonucleotide therapeutics. In both approaches, fibroblasts were the most susceptible to locally delivered ASOs, with significant silencing also in endothelial cells. Third, we confirmed that the robust silencing in fibroblasts is broadly applicable by silencing two targets expressed mainly in fibroblasts, Mfap4 and Adam33. Across independent approaches, we demonstrate that intratracheally administered LNA gapmer ASOs robustly induce gene silencing in lung fibroblasts. ASO-induced gene silencing in fibroblasts was durable, lasting 4-8 weeks after a single dose. Thus, lung fibroblasts are well aligned with ASOs as therapeutics., (© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Microbial communities are shaped by viral predators. Yet, resolving which viruses (phages) and bacteria are interacting is a major challenge in the context of natural levels of microbial diversity. Thus, fundamental features of how phage-bacteria interactions are structured and evolve in the wild remain poorly resolved. Here we use large-scale isolation of environmental marine Vibrio bacteria and their phages to obtain estimates of strain-level phage predator loads, and use all-by-all host range assays to discover how phage and host genomic diversity shape interactions. We show that lytic interactions in environmental interaction networks (as observed in agar overlay) are sparse-with phage predator loads being low for most bacterial strains, and phages being host-strain-specific. Paradoxically, we also find that although overlap in killing is generally rare between tailed phages, recombination is common. Together, these results suggest that recombination during cryptic co-infections is an important mode of phage evolution in microbial communities. In the development of phages for bioengineering and therapeutics it is important to consider that nucleic acids of introduced phages may spread into local phage populations through recombination, and that the likelihood of transfer is not predictable based on lytic host range., (© 2022. The Author(s).)

Objective: To investigate the incidence of LARS in patients undergoing elective anterior resection within the MRC/NIHR ROLARR trial and to explore perioperative variables that might be associated with major LARS., Summary Background Data: Sphincter-preserving rectal cancer surgery is frequently accompanied by defaecatory dysfunction known as Low anterior resection syndrome (LARS). This is distressing for patients and is an unmet clinical challenge., Methods: An international, retrospective cohort study of patients undergoing anterior resection within the ROLARR trial was undertaken. Trial participants with restoration of gastrointestinal continuity and free from disease recurrence completed the validated LARS questionnaire between August 2015 and April 2017. The primary outcome was the incidence of LARS and secondary outcome was severity (minor versus major)., Results: LARS questionnaires were received from 132/155 (85%) eligible patients. The median time from surgery to LARS assessment was 1065 days (range 174-1655 d). The incidence of LARS was 82.6% (n = 109/132), which was minor in 26/132 (19.7%) and major in 83/132 (62.9%). The most common symptoms were incontinence to flatus (n = 86/132; 65.2%) and defaecatory clustering (88/132; 66.7%). In a multivariate model, predictors of major LARS were: 1 cm decrease in tumor height above the anal verge (OR = 1.290, 95% CI: 1.101,1.511); and an ASA grade greater than 1 (OR = 2.920, 95% CI: 1.239, 6.883). Treatment allocation (laparoscopic vs robotic) did not predict major LARS., Conclusions: LARS is a common after rectal cancer surgery and patients should be appropriately counselled preoperatively, particularly before surgery for low tumors or in comorbid populations., Competing Interests: The authors report no conflicts of interest., (Copyright © 2020 Wolters Kluwer Health, Inc. All rights reserved.)

Sulfate-reducing bacteria Candidatus Desulforudis audaxviator (CDA) were originally discovered in deep fracture fluids accessed via South African gold mines and have since been found in geographically widespread deep subsurface locations. In order to constrain models for subsurface microbial evolution, we compared CDA genomes from Africa, North America and Eurasia using single cell genomics. Unexpectedly, 126 partial single amplified genomes from the three continents, a complete genome from of an isolate from Eurasia, and metagenome-assembled genomes from Africa and Eurasia shared >99.2% average nucleotide identity, low frequency of SNP's, and near-perfectly conserved prophages and CRISPRs. Our analyses reject sample cross-contamination, recent natural dispersal, and unusually strong purifying selection as likely explanations for these unexpected results. We therefore conclude that the analyzed CDA populations underwent only minimal evolution since their physical separation, potentially as far back as the breakup of Pangea between 165 and 55 Ma ago. High-fidelity DNA replication and repair mechanisms are the most plausible explanation for the highly conserved genome of CDA. CDA presents a stark contrast to the current model organisms in microbial evolutionary studies, which often develop adaptive traits over far shorter periods of time., (© 2021. The Author(s).)

Viruses are traditionally thought to be under selective pressure to maintain compact genomes and thus depend on host cell translational machinery for reproduction. However, some viruses encode abundant tRNA and other translation-related genes, potentially optimizing for codon usage differences between phage and host. Here, we systematically interrogate selective advantages that carrying 18 tRNAs may convey to a T4-like Vibriophage. Host DNA and RNA degrade upon infection, including host tRNAs, which are replaced by those of the phage. These tRNAs are expressed at levels slightly better adapted to phage codon usage, especially that of late genes. The phage is unlikely to randomly acquire as diverse an array of tRNAs as observed (p = 0.0017). Together, our results support that the main driver behind phage tRNA acquisition is pressure to sustain translation as host machinery degrades, a process resulting in a dynamically adapted codon usage strategy during the course of infection., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Background and Purpose: Multi-arm non-inferiority (MANI) trials, here defined as non-inferiority trials with multiple experimental treatment arms, can be useful in situations where several viable treatments exist for a disease area or for testing different dose schedules. To maintain the statistical integrity of such trials, issues regarding both design and analysis must be considered, from both the multi-arm and the non-inferiority perspectives. Little guidance currently exists on exactly how these aspects should be addressed and it is the aim of this paper to provide recommendations to aid the design of future MANI trials., Methods: A comprehensive literature review covering four databases was conducted to identify publications associated with MANI trials. Literature was split into methodological and trial publications in order to investigate the required design and analysis considerations for MANI trials and whether they were being addressed in practice., Results: A number of issues were identified that if not properly addressed, could lead to issues with the FWER, power or bias. These ranged from the structuring of trial hypotheses at the design stage to the consideration of potential heterogeneous treatment variances at the analysis stage. One key issue of interest was adjustment for multiple testing at the analysis stage. There was little consensus concerning whether more powerful p value adjustment methods were preferred to approximate adjusted CIs when presenting and interpreting the results of MANI trials. We found 65 examples of previous MANI trials, of which 31 adjusted for multiple testing out of the 39 that were adjudged to require it. Trials generally preferred to utilise simple, well-known methods for study design and analysis and while some awareness was shown concerning FWER inflation and choice of power, many trials seemed not to consider the issues and did not provide sufficient definition of their chosen design and analysis approaches., Conclusions: While MANI trials to date have shown some awareness of the issues raised within this paper, very few have satisfied the criteria of the outlined recommendations. Going forward, trials should consider the recommendations in this paper and ensure they clearly define and reason their choices of trial design and analysis techniques.

Background: Preliminary studies using the FENIX™ (Torax Medical, Minneapolis, MN, USA) magnetic sphincter augmentation device suggest that it is safe to use for the treatment of adult faecal incontinence, but efficacy data are limited., Objective: To compare FENIX with sacral nerve stimulation for the treatment of adult faecal incontinence in terms of safety, efficacy, quality of life and cost-effectiveness., Design, Setting and Participants: Multicentre, parallel-group, unblinded, randomised trial comparing FENIX with sacral nerve stimulation in participants suffering moderate to severe faecal incontinence., Interventions: Participants were randomised on an equal basis to either sacral nerve stimulation or FENIX. Follow-up occurred 2 weeks postoperatively and at 6, 12 and 18 months post randomisation., Main Outcome and Measure: The primary outcome was success, defined as device in use and ≥ 50% improvement in Cleveland Clinic Incontinence Score at 18 months post randomisation. Secondary outcomes included complication rates, quality of life and cost-effectiveness. Between 30 October 2014 and 23 March 2017, 99 participants were randomised across 18 NHS sites (50 participants to FENIX vs. 49 participants to sacral nerve stimulation). The median time from randomisation to FENIX implantation was 57.0 days (range 4.0-416.0 days), and the median time from randomisation to permanent sacral nerve stimulation was 371.0 days (range 86.0-918.0 days). A total of 45 out of 50 participants underwent FENIX implantation and 29 out of 49 participants continued to permanent sacral nerve stimulation. The following results are reported, excluding participants for whom the corresponding outcome was not evaluable. Overall, there was success for 10 out of 80 (12.5%) participants, with no statistically significant difference between the two groups [FENIX 6/41 (14.6%) participants vs. sacral nerve stimulation 4/39 (10.3%) participants]. At least one postoperative complication was experienced by 33 out of 45 (73.3%) participants in the FENIX group and 9 out of 40 (22.5%) participants in the sacral nerve stimulation group. A total of 15 out of 50 (30%) participants in the FENIX group ultimately had to have their device explanted. Slightly higher costs and quality-adjusted life-years (incremental = £305.50 and 0.005, respectively) were observed in the FENIX group than in the sacral nerve stimulation group. This was reversed over the lifetime horizon (incremental = -£1306 and -0.23 for costs and quality-adjusted life-years, respectively), when sacral nerve stimulation was the optimal option (net monetary benefit = -£3283), with only a 45% chance of FENIX being cost-effective., Limitations: The SaFaRI study was terminated in 2017, having recruited 99 participants of the target sample size of 350 participants. The study is, therefore, substantially underpowered to detect differences between the treatment groups, with significant uncertainty in the cost-effectiveness analysis., Conclusions: The SaFaRI study revealed inefficiencies in the treatment pathways for faecal incontinence, particularly for sacral nerve stimulation. The success of both FENIX and sacral nerve stimulation was much lower than previously reported, with high postoperative morbidity in the FENIX group., Future Work: Further research is needed to clarify the treatment pathways for sacral nerve stimulation and to determine its true clinical and cost-effectiveness., Trial Registration: Current Controlled Trials ISRCTN16077538., Funding: This project was funded by the National Institute for Health Research (NIHR) Health Technology Assessment programme and will be published in full in Health Technology Assessment ; Vol. 25, No. 18. See the NIHR Journals Library website for further project information.

The Myeloma X trial (ISCRTN60123120) registered patients with relapsed multiple myeloma. Participants were randomised between salvage autologous stem cell transplantation (ASCT) or weekly cyclophosphamide following re-induction therapy. Cytogenetic analysis performed at trial registration defined t(4;14), t(14;16) and del(17p) as high-risk. The effect of cytogenetics on time to progression (TTP) and overall survival was investigated. At 76 months median follow-up, ASCT improved TTP compared to cyclophosphamide (19 months (95% confidence interval [95% CI] 16-26) vs. 11 months (9-12), hazard ratio [HR]: 0·40, 95% CI: 0·29-0·56, P < 0·001), on which the presence of any single high-risk lesion had a detrimental impact [likelihood ratio test (LRT): P = 0·011]. ASCT also improved OS [67 months (95% CI 59-not reached) vs. 55 months (44-67), HR: 0·64, 95% CI: 0·42-0·99, P = 0·0435], with evidence of a detrimental impact with MYC rearrangement (LRT: P = 0·021). Twenty-one (24·7%) cyclophosphamide patients received an ASCT post-trial, median OS was not reached (95% CI: 39-not reached) for these participants compared to 31 months (22-39), in those who did not receive a post-trial ASCT. The analysis further supports the benefit of salvage ASCT, which may still be beneficial after second relapse in surviving patients. There is evidence that this benefit reduces in cytogenetic high-risk patients, highlighting the need for targeted study in this patient group., (© 2019 The Authors. British Journal of Haematology published by British Society for Haematology and John Wiley & Sons Ltd.)

Introduction: Pressure ulcer-specific patient-reported outcome (PRO) instruments should be used to inform patient care and provide a strong evidence base for interventions aimed at preventing pressure ulcers. The aim was to carry out a comprehensive evaluation of the psychometric properties of a PRO instrument designed to assess symptoms and functional outcomes in patients at high-risk of developing pressure ulcers, the PU-QOL-P instrument., Methods: We modified the original PU-QOL instrument to be suitable for patients at high risk of pressure ulcer development based on feedback from patients, specialist nurses and PRO methodologists. The modified PU-QOL-P instrument was administered to a sub-set of patients participating in the PRESSURE 2 trial. Patients completed PU-QOL-P and SF12 instruments at baseline, weeks 1 and 3, and 30 days post-treatment. We undertook psychometric evaluation of the modified PU-QOL-P to test scale targeting, scaling assumptions, reliability, validity and responsiveness., Results: The analysis sample consisted of 617 patients that completed both instruments at baseline. We found that the PU-QOL-P instrument, consisting of nine PU-specific outcomes: three symptom and six function scales, meets established criteria for reliability, construct validity, and responsiveness. Internal consistency reliability was high with all scale Cronbach alpha > 0.795 (range 0.795-0.970). The factor analysis mostly supported the six-function scale structure. Scaling assumptions were satisfied; all item-total correlations above 0.30. Convergent validity was confirmed by significant correlations between hypothesized scales as expected. PU-QOL-P scales were responsive to change: mean scale scores from baseline to 30 days post-treatment were statistically significant for all scales apart the daily activities scale (effect sizes ranged from moderate to high). As expected, worse symptoms and functioning was observed in patients who had a category 1 or 2 PU compared to patients who did not have a PU., Conclusions: The PU-QOL-P provides a standardised method for assessing pressure ulcer-specific symptoms and functional outcomes for quantifying the benefits of associated interventions from the patient's perspective. It can be used in research with adults at risk of pressure ulcer development in all UK healthcare settings.

Introduction: Patient-reported outcomes (PROs) are increasingly included within cancer clinical trials. If appropriately collected, analysed and transparently reported, these data might provide invaluable evidence to inform patient care. However, there is mounting indication that the design and reporting of PRO data in cancer trials may be suboptimal. This programme of research will establish via three interlinked studies whether these findings are applicable to UK cancer trials, and if so, how to best enhance the way PROs are assessed, managed and reported in clinical trials. This study will explore with key stakeholders factors that influence optimal PRO protocol content, implementation and reporting and make recommendations for training and guidance., Methods and Analysis: Semistructured interviews will be conducted with members of key stakeholder groups. The purposive sample of up to 48 participants will include: (1) trial chief investigators, trial management group members, statisticians and research nurses of cancer trials including primary or secondary PRO recruited via the National Cancer Research Institute (NCRI) Clinical Studies Group and Consumer Liaison Group and the UK Clinical Research Collaboration Registered UK Clinical Trial Unit Network; (2) NCRI Consumer Liaison Group members; (3) international experts in PRO oncology trial design; and (4) journal editors and funding bodies. Data will be analysed using directed thematic analysis employing a coding frame and modified as analysis progresses. Formal triangulation of coding and member checking will be employed to enhance credibility., Ethics and Dissemination: This study was approved by the University of Birmingham Ethics Committee (Ref: ERN&#95;17-0085). Findings will be disseminated via conference presentations, peer-reviewed journals, patient groups and social media (@CPROR&#95;UoB; http://www.birmingham.ac.uk/cpror)., Prospero Registration Number: CRD42016036533., Competing Interests: Competing interests: JA, LC, CC, AnG, AdG, DMG, DK and AL are all members of the National Cancer Research Institute Psychosocial Oncology and Survivorship CSG subgroup: ‘Understanding and measuring the consequences of cancer and its treatment’. FE receives consultancy fees from Bristol-Myers Squibb, Seattle Genetics, TEVA and Incyte; and research funding from Lundbeck, TEVA and Amgen. GV receives grants from the National Institute for Health Research and Yorkshire Cancer Research, and personal fees from Roche, Genentech, Eisai and Novartis. MC has received personal fees from Astellas Pharma and Ferring and chairs the ISOQOL Best Practice for PROs in Trials Taskforce. JMB receives grants from the National Institute of Health Research, Yorkshire Cancer Research, Macmillan and Roche. JA is in receipt of grant funding from EU FP7 Framework. AdG is in receipt of grants from Candlelighters, National Institute for Health Research, Macmillan Cancer Support, Prostate Cancer UK and Yorkshire Cancer Research. MTK and RM-B have received project funding from Abbvie and Alcon. MTK cochairs the ISOQOL Best Practice for PROs in Trials Taskforce. DK and RM-B are members of the ISOQOL Best Practice for PROs in Trials Taskforce., (© Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.)

The most abundant viruses on Earth are thought to be double-stranded DNA (dsDNA) viruses that infect bacteria. However, tailed bacterial dsDNA viruses (Caudovirales), which dominate sequence and culture collections, are not representative of the environmental diversity of viruses. In fact, non-tailed viruses often dominate ocean samples numerically, raising the fundamental question of the nature of these viruses. Here we characterize a group of marine dsDNA non-tailed viruses with short 10-kb genomes isolated during a study that quantified the diversity of viruses infecting Vibrionaceae bacteria. These viruses, which we propose to name the Autolykiviridae, represent a novel family within the ancient lineage of double jelly roll (DJR) capsid viruses. Ecologically, members of the Autolykiviridae have a broad host range, killing on average 34 hosts in four Vibrio species, in contrast to tailed viruses which kill on average only two hosts in one species. Biochemical and physical characterization of autolykiviruses reveals multiple virion features that cause systematic loss of DJR viruses in sequencing and culture-based studies, and we describe simple procedural adjustments to recover them. We identify DJR viruses in the genomes of diverse major bacterial and archaeal phyla, and in marine water column and sediment metagenomes, and find that their diversity greatly exceeds the diversity that is currently captured by the three recognized families of such viruses. Overall, these data suggest that viruses of the non-tailed dsDNA DJR lineage are important but often overlooked predators of bacteria and archaea that impose fundamentally different predation and gene transfer regimes on microbial systems than on tailed viruses, which form the basis of all environmental models of bacteria-virus interactions.

Recent advances in single-cell genomic and metagenomic techniques have facilitated the discovery of numerous previously unknown, deep branches of the tree of life that lack cultured representatives. Many of these candidate phyla are composed of microorganisms with minimalistic, streamlined genomes lacking some core metabolic pathways, which may contribute to their resistance to growth in pure culture. Here we analyzed single-cell genomes and metagenome bins to show that the "Candidate phylum Rokubacteria," formerly known as SPAM, represents an interesting exception, by having large genomes (6-8 Mbps), high GC content (66-71%), and the potential for a versatile, mixotrophic metabolism. We also observed an unusually high genomic heterogeneity among individual Rokubacteria cells in the studied samples. These features may have contributed to the limited recovery of sequences of this candidate phylum in prior cultivation and metagenomic studies. Our analyses suggest that Rokubacteria are distributed globally in diverse terrestrial ecosystems, including soils, the rhizosphere, volcanic mud, oil wells, aquifers, and the deep subsurface, with no reports from marine environments to date.

Microbial single-cell genomics can be used to provide insights into the metabolic potential, interactions, and evolution of uncultured microorganisms. Here we present WGA-X, a method based on multiple displacement amplification of DNA that utilizes a thermostable mutant of the phi29 polymerase. WGA-X enhances genome recovery from individual microbial cells and viral particles while maintaining ease of use and scalability. The greatest improvements are observed when amplifying high G+C content templates, such as those belonging to the predominant bacteria in agricultural soils. By integrating WGA-X with calibrated index-cell sorting and high-throughput genomic sequencing, we are able to analyze genomic sequences and cell sizes of hundreds of individual, uncultured bacteria, archaea, protists, and viral particles, obtained directly from marine and soil samples, in a single experiment. This approach may find diverse applications in microbiology and in biomedical and forensic studies of humans and other multicellular organisms.Single-cell genomics can be used to study uncultured microorganisms. Here, Stepanauskas et al. present a method combining improved multiple displacement amplification and FACS, to obtain genomic sequences and cell size information from uncultivated microbial cells and viral particles in environmental samples.

Introduction: Emerging evidence suggests that patient-reported outcome (PRO)-specific information may be omitted in trial protocols and that PRO results are poorly reported, limiting the use of PRO data to inform cancer care. This study aims to evaluate the standards of PRO-specific content in UK cancer trial protocols and their arising publications and to highlight examples of best-practice PRO protocol content and reporting where they occur. The objective of this study is to determine if these early findings are generalisable to UK cancer trials, and if so, how best we can bring about future improvements in clinical trials methodology to enhance the way PROs are assessed, managed and reported., Hypothesis: Trials in which the primary end point is based on a PRO will have more complete PRO protocol and publication components than trials in which PROs are secondary end points., Methods and Analysis: Completed National Institute for Health Research (NIHR) Portfolio Cancer clinical trials (all cancer specialities/age-groups) will be included if they contain a primary/secondary PRO end point. The NIHR portfolio includes cancer trials, supported by a range of funders, adjudged as high-quality clinical research studies. The sample will be drawn from studies completed between 31 December 2000 and 1 March 2014 (n=1141) to allow sufficient time for completion of the final trial report and publication. Two reviewers will then review the protocols and arising publications of included trials to: (1) determine the completeness of their PRO-specific protocol content; (2) determine the proportion and completeness of PRO reporting in UK Cancer trials and (3) model factors associated with PRO protocol and reporting completeness and with PRO reporting proportion., Ethics and Dissemination: The study was approved by the ethics committee at University of Birmingham (ERN&#95;15-0311). Trial findings will be disseminated via presentations at local, national and international conferences, peer-reviewed journals and social media including the CPROR twitter account and UOB departmental website (http://www.birmingham.ac.uk/cpro0r)., Trial Registration Number: PROSPERO CRD42016036533., (Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/)

Background: The Myeloma X trial previously reported improved durability of response (time to disease progression) in patients with relapsed multiple myeloma with salvage autologous stem-cell transplantation (ASCT) compared with oral cyclophosphamide in patients with multiple myeloma relapsing after a first ASCT. We report the final overall survival results of the trial., Methods: BSBMT/UKMF Myeloma X was a multicentre, randomised, open-label, phase 3 trial done at 51 centres in the UK. Eligible patients with multiple myeloma relapsing after a previous ASCT were re-induced with intravenous bortezomib (1·3 mg/m(2) on days 1, 4, 8, 11), intravenous doxorubicin (9 mg/m(2) per day on days 1-4), and oral dexamethasone (40 mg/day on days 1-4, 8-11, and 15-18 during cycle 1 and days 1-4 during cycles 2-4), with supportive care as per local institutional protocols before randomisation in a 1:1 ratio to either high-dose melphalan (200 mg/m(2)) and salvage ASCT or weekly oral cyclophosphamide (400 mg/m(2) per week for 12 weeks). Randomisation was by permuted blocks stratified by length of first remission and response to re-induction treatment. The primary endpoint was time to disease progression; the study was also powered to detect a difference in the secondary endpoint, overall survival. Further secondary endpoints were the proportion of patients achieving an objective response, progression-free survival, overall survival, toxic effects and safety, pain, and quality of life. Prespecified exploratory endpoints included time to second objective disease progression (PFS2). Analysis was by intention to treat. This trial is registered with ClinicalTrials.gov, number NCT00747877, and the European Clinical Trials Database, number 2006-005890-24, and is now in long-term follow-up., Findings: Between April 16, 2008, and Nov 19, 2012, 297 patients were registered into the study and 174 were randomly assigned to receive either high-dose melphalan and salvage ASCT (n=89) or oral weekly cyclophosphamide (n=85). 173 (58%) of 297 patients relapsed after more than 24 months from first ASCT. 75 (43%) of 174 randomised patients had died at follow-up: salvage ASCT (n=31 [35%]) versus oral weekly cyclophosphamide (n=44 [52%]). Updated time to disease progression shows continued advantage in the salvage ASCT group compared with the weekly cyclophosphamide group (19 months [95% CI 16-26] vs 11 months [9-12]; hazard ratio [HR] 0·45 [95% CI 0·31-0·64] log-rank p<0·0001). Median overall survival was superior in the salvage ASCT group compared with weekly cyclophosphamide group (67 months [95% CI 55-not estimable] vs 52 months [42-60]; log-rank p=0·022; HR 0·56 [0·35-0·90], p=0·0169). Time to second objective disease progression was superior in the salvage ASCT group compared with the weekly cyclophosphamide group (67 months [52-not estimable] vs 35 months [31-43]; HR 0·37 [0·24-0·57], log-rank p<0·0001). During extended follow-up, no further treatment-related or treatment-unrelated adverse events were reported. 15 second primary malignancies were reported in 12 patients (salvage ASCT [n=7] vs oral weekly cyclophosphamide [n=5]). The cumulative incidence of second primary malignancies at 60 months after trial entry was 5·2% (2·1-8·2)., Interpretation: Salvage ASCT increases overall survival during consolidation of re-induction treatment in patients with multiple myeloma at first relapse after a first ASCT. The delay of salvage ASCT to third-line treatment or later might not confer the same degree of advantage as seen with salvage ASCT at first relapse., Funding: Cancer Research UK, Janssen-Cilag, and Chugai Pharma UK., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

Purpose: To examine factors associated with false-negative cardiovascular magnetic resonance (MR) perfusion studies within the large prospective Clinical Evaluation of MR imaging in Coronary artery disease (CE-MARC) study population. Myocardial perfusion MR has excellent diagnostic accuracy to detect coronary heart disease (CHD). However, causes of false-negative MR perfusion studies are not well understood., Materials and Methods: CE-MARC prospectively recruited patients with suspected CHD and mandated MR, myocardial perfusion scintigraphy, and invasive angiography. This subanalysis identified all patients with significant coronary stenosis by quantitative coronary angiography (QCA) and MR perfusion (1.5T, T1 -weighted gradient echo), using the original blinded image read. We explored patient and imaging characteristics related to false-negative or true-positive MR perfusion results, with reference to QCA. Multivariate regression analysis assessed the likelihood of false-negative MR perfusion according to four characteristics: poor image quality, triple-vessel disease, inadequate hemodynamic response to adenosine, and Duke jeopardy score (angiographic myocardium-at-risk score)., Results: In all, 265 (39%) patients had significant angiographic disease (mean age 62, 79% male). Thirty-five (5%) had false-negative and 230 (34%) true-positive MR perfusion. Poor MR perfusion image quality, triple-vessel disease, and inadequate hemodynamic response were similar between false-negative and true-positive groups (odds ratio, OR [95% confidence interval, CI]: 4.1 (0.82-21.0), P = 0.09; 1.2 (0.20-7.1), P = 0.85, and 1.6 (0.65-3.8), P = 0.31, respectively). Mean Duke jeopardy score was significantly lower in the false-negative group (2.6 ± 1.7 vs. 5.4 ± 3.0, OR 0.34 (0.21-0.53), P < 0.0001)., Conclusion: False-negative cardiovascular MR perfusion studies are uncommon, and more common in patients with lower angiographic myocardium-at-risk. In CE-MARC, poor image quality, triple-vessel disease, and inadequate hemodynamic response were not significantly associated with false-negative MR perfusion., (© 2015 The Authors Journal of Magnetic Resonance Imaging published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine.)

Purpose: Faecal incontinence is a physically, psychologically and socially disabling condition. NICE guidance (2007) recommends surgical intervention, including sacral nerve stimulation (SNS), after failed conservative therapies. The FENIX magnetic sphincter augmentation (MSA) device is a novel continence device consisting of a flexible band of interlinked titanium beads with magnetic cores that is placed around the anal canal to augment anal sphincter tone through passive attraction of the beads. Preliminary studies suggest the FENIX MSA is safe, but efficacy data is limited. Rigorous evaluation is required prior to widespread adoption., Method and Design: The SaFaRI trial is a National Institute of Health Research (NIHR) Health Technology Assessment (HTA)-funded UK multi-site, parallel group, randomised controlled, unblinded trial that will investigate the use of the FENIX MSA, as compared to SNS, for adult faecal incontinence resistant to conservative management. Twenty sites across the UK, experienced in the treatment of faecal incontinence, will recruit 350 patients randomised equally to receive either SNS or FENIX MSA. Participants will be followed-up at 2 weeks post-surgery and at 6, 12 and 18 months post-randomisation. The primary endpoint is success, as defined by device in use and ≥50 % improvement in the Cleveland Clinic Incontinence Score (CCIS) at 18 months post-randomisation. Secondary endpoints include complications, quality of life and cost effectiveness., Discussion: SaFaRI will rigorously evaluate a new technology for faecal incontinence, the FENIX™ MSA, allowing its safe and controlled introduction into current clinical practice. These results will inform the future surgical management of adult faecal incontinence.

Strain HIMB11 is a planktonic marine bacterium isolated from coastal seawater in Kaneohe Bay, Oahu, Hawaii belonging to the ubiquitous and versatile Roseobacter clade of the alphaproteobacterial family Rhodobacteraceae. Here we describe the preliminary characteristics of strain HIMB11, including annotation of the draft genome sequence and comparative genomic analysis with other members of the Roseobacter lineage. The 3,098,747 bp draft genome is arranged in 34 contigs and contains 3,183 protein-coding genes and 54 RNA genes. Phylogenomic and 16S rRNA gene analyses indicate that HIMB11 represents a unique sublineage within the Roseobacter clade. Comparison with other publicly available genome sequences from members of the Roseobacter lineage reveals that strain HIMB11 has the genomic potential to utilize a wide variety of energy sources (e.g. organic matter, reduced inorganic sulfur, light, carbon monoxide), while possessing a reduced number of substrate transporters.

Purpose: There is growing enthusiasm for robotic-assisted laparoscopic operations across many surgical specialities, including colorectal surgery, often not supported by robust clinical or cost-effectiveness data. A proper assessment of this new technology is required, prior to widespread recommendation or implementation., Methods/design: The ROLARR trial is a pan-world, prospective, randomised, controlled, unblinded, superiority trial of robotic-assisted versus standard laparoscopic surgery for the curative treatment of rectal cancer. It will investigate differences in terms of the rate of conversion to open operation, rate of pathological involvement of circumferential resection margin, 3-year local recurrence, disease-free and overall survival rates and also operative morbidity and mortality, quality of life and cost-effectiveness. The primary outcome measure is the rate of conversion to open operation. For 80% power at the 5% (two-sided) significance level, to identify a relative 50% reduction in open conversion rate (25% to 12.5%), 336 patients will be required. The target recruitment is 400 patients overall to allow loss to follow-up. Patients will be followed up at 30 days and 6 months post-operatively and then annually until 3 years after the last patient has been randomised., Discussion: In many centres, robotic-assisted surgery is being implemented on the basis of theoretical advantages, which have yet to be confirmed in practice. Robotic surgery is an expensive health care provision and merits robust evaluation. The ROLARR trial is a pragmatic trial aiming to provide a comprehensive evaluation of both robotic-assisted and standard laparoscopic surgery for the curative resection of rectal cancer.

Viruses in aquatic ecosystems comprise those produced by both autochthonous and allochthonous host taxa. However, there is little information on the diversity and abundance of viruses of allochthonous origin, particularly from non-anthropogenic sources, in freshwater and marine ecosystems. We investigated the presence of nucleopolyhedroviruses (NPV) (Baculovirus), which commonly infect terrestrial lepidopteran taxa, across the landscape of Appledore Island, Gulf of Maine. PCR and qPCR primers were developed around a 294-bp fragment of the polyhedrin (polH) gene, which is the major constituent protein of NPV multivirion polyhedral occlusion bodies. polH was successfully amplified from several aquatic habitats, and recovered polH sequences were most similar to known lepidopteran NPV. Using quantitative PCR designed around a cluster of detected sequences, we detected polH in Appledore Island soils, supratidal freshwater ponds, nearshore sediments, near- and offshore plankton, and in floatsam. This diverse set of locations suggests that NPVs are widely dispersed along the terrestrial--marine continuum and that free polyhedra may be washed into ponds and eventually to sea. The putative hosts of detected NPVs were webworms (Hyphantria sp.) which form dense nests in late summer on the dominant Appledore Island vegetation (Prunus virginiana). Our data indicate that viruses of terrestrial origin (i.e., allochthonous viruses) may be dispersed widely in coastal marine habitats. The dispersal of NPV polH and detection within offshore net plankton (>64 μm) demonstrates that terrestrial viruses may interact with larger particles and plankton of coastal marine ecosystem, which further suggests that viral genomic information may be transported between biomes.

Unlabelled: This multicenter study assessed the feasibility of conducting a phase III trial of transcutaneous electrical nerve stimulation (TENS) in patients with cancer bone pain recruited from palliative care services. Eligible patients received active and placebo TENS for 1 hour at site of pain in a randomized crossover design; median interval between applications 3 days. Responses assessed at 30 and 60 minutes included numerical and verbal ratings of pain at rest and on movement, and pain relief. Recruitment, tolerability, adverse events, and effectiveness of blinding were also evaluated. Twenty-four patients were randomised and 19 completed both applications. The intervention was well tolerated. Five patients withdrew: 3 due to deteriorating performance status, and 2 due to increased pain (1 each following active and placebo TENS). Confidence interval estimation around the differences in outcomes between active and placebo TENS suggests that TENS has the potential to decrease pain on movement more than pain on rest. Nine patients did not consider that a placebo was used; the remaining 10 correctly identified placebo TENS. Feasibility studies are important in palliative care prior to undertaking clinical trials. Our findings suggest that further work is required on recruitment strategies and refining the control arm before evaluating TENS in cancer bone pain., Perspective: Cancer bone pain is common and severe, and partly mediated by hyperexcitability. Animal studies suggest that Transcutaneous Electrical Nerve Stimulation can reduce hyperalgesia. This study examined the feasibility of evaluating TENS in patients with cancer bone pain in order to optimize methods before a phase III trial., (Copyright 2010 American Pain Society. Published by Elsevier Inc. All rights reserved.)

Background: Several investigations are currently available to establish the diagnosis of coronary heart disease (CHD). Of these, cardiovascular magnetic resonance (CMR) offers the greatest information from a single test, allowing the assessment of myocardial function, perfusion, viability and coronary artery anatomy. However, data from large scale studies that prospectively evaluate the diagnostic accuracy of multi-parametric CMR for the detection of CHD in unselected populations are lacking, and there are few data on the performance of CMR compared with current diagnostic tests, its prognostic value and cost-effectiveness., Methods/design: This is a prospective diagnostic accuracy cohort study of 750 patients referred to a cardiologist with suspected CHD. Exercise tolerance testing (ETT) will be preformed if patients are physically able. Recruited patients will then undergo CMR and single photon emission tomography (SPECT) followed in all patients by invasive X-ray coronary angiography. The order of the CMR and SPECT tests will be randomised. The CMR study will comprise rest and adenosine stress perfusion, cine imaging, late gadolinium enhancement and whole-heart MR coronary angiography. SPECT will use a gated stress/rest protocol. The primary objective of the study is to determine the diagnostic accuracy of CMR in detecting significant coronary stenosis, as defined by X-ray coronary angiography. Secondary objectives include an assessment of the prognostic value of CMR imaging, a comparison of its diagnostic accuracy against SPECT and ETT, and an assessment of cost-effectiveness., Discussion: The CE-MARC study is a prospective, diagnostic accuracy cohort study of 750 patients assessing the performance of a multi-parametric CMR study in detecting CHD using invasive X-ray coronary angiography as the reference standard and comparing it with ETT and SPECT., Trial Registration: Current Controlled Trials ISRCTN77246133.

Purpose: Options for single-agent fluoropyrimidine adjuvant therapy after bowel cancer resection include intravenous fluorouracil with leucovorin (FU/LV) or oral capecitabine. These treatments have similar efficacy but differ in convenience and toxicity. We therefore wished to compare their overall acceptability to patients., Patients and Methods: Patients scheduled for adjuvant single-agent fluoropyrimidine therapy were randomly assigned to receive once-weekly FU/LV (425 mg/m(2) FU, 45 mg LV) for 6 weeks, followed by two 3-week cycles of capecitabine (1,250 mg/m(2) twice daily, days 1 through 14), or the same treatments but in reverse order. After 12 weeks, the patients were asked which treatment they preferred, and received the preferred treatment for an additional 12 weeks. The primary end point was patient preference., Results: After 40 of the planned 74 patients had been randomly assigned, real-time adverse event monitoring led to early trial closure because of excess sequence-specific toxicity. Eleven of 14 patients (79%) receiving capecitabine as their second treatment experienced grade >/= 3 toxicity. This compared with five of 18 patients (28%) receiving capecitabine as the first treatment, and no patients receiving FU/LV as the first treatment (zero of 16) or the second treatment (zero of 12). Similar imbalances were seen in the proportion of patients requiring interruption of treatment., Conclusion: In chemotherapy-naïve patients, capecitabine produced more toxicity than FU/LV, but at levels in line with previously reported data. However, treatment with capecitabine after FU/LV caused markedly increased toxicity, indicating a sequence-specific interaction. The mechanism has not been determined, but interaction with intracellularly retained folate after FU/LV therapy is a possibility. Oncologists need to be aware of this risk if considering crossing patients over from FU/LV to capecitabine-based regimens.

A diagnosis of gynaecological cancer and its treatment are usually associated with many physical and psychological changes, both as a result of the diagnosis itself and of the usual treatments of surgery, radiotherapy and/or several months of chemotherapy. Patients often experience symptoms such as fatigue, abdominal swelling and pain, and suffer from emotional distress and disturbances of their life style. Sexual functioning can also be affected. Often there are physiological difficulties, such as vaginal dryness, together with psychological distress and relationship problems. This chapter discusses the ways in which gynaecological cancer can impact sexual functioning, and presents findings from a research project that was undertaken to begin to understand how sexual functioning can be affected by ovarian cancer. The article also makes recommendations for how health-care professionals can help women to cope better with psychosexual dysfunction following a diagnosis of a gynaecological cancer.