Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution.

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Effect of use of proton pump inhibitors on serum magnesium levels in older people:an observational study

No abstract availabl

The views of older people and carers on participation in clinical trials: the PREDICT Study

Concern over the inappropriate exclusion of older people from clinical trials is longstanding. The PREDICT study used mixed methods to investigate the extent of this exclusion and to explore the views of those directly involved. This paper reports findings from that aspect of the study investigating the views of older people and carers. Drawing on findings from earlier stages in the study, a structured interview schedule was developed to form the basis of focus group discussions. Groups were held across nine countries: the Czech Republic, Israel, Italy, Lithuania, Holland, Poland, Romania, Spain and the UK (n = 42). Discussants were those living with conditions commonly affecting older people: hypertension, cancer, dementia, heart failure, stroke and depression (n = 285). Data were analyzed for differences and commonalities within and between groups. Issues raised fell into four themes: ageism, both within society and amongst clinicians and researchers; advantages and disadvantages to participation; the relationship between the participant and their clinician/research team; and practical features to support participation. Findings confirm that older people and carers see chronological age as an insufficient reason for exclusion from trials and view such exclusion as age discrimination. They point to the complex relationship between healthcare professionals and trial participants and identify the need for cultural and generational sensitivity in trial design, as well as the importance of considering adaptations to meet special needs. Finally, they identify the need for quality of life to be included as an outcome measure in such research and emphasize the importance of including lay perspectives in health research design generally

The representation of elderly patients in clinical trials – presentation of assumptions of PREDICT project

Wstęp. Liczne doniesienia wskazują na małą i nierówną reprezentację osób starszych w badaniach klinicznych stanowiących podstawę tworzenia zaleceń dotyczących postępowania. Stało się to przesłanką do przeprowadzenia wieloośrodkowego, międzynarodowego programu badawczego „Zwiększanie udziału osób starszych w badaniach klinicznych” (PREDICT), finansowanego przez Komisję Europejską w ramach VII Projektu Ramowego. Celem projektu było rozpoznanie przyczyn i skali zjawiska oraz stworzenie zaleceń odnośnie do włączania osób w starszym wieku do badań. Materiał i metody. W projekcie uczestniczyło 11 instytucji z 9 krajów: Czech, Hiszpanii, Holandii, Izraela, Litwy, Polski, Rumunii, Wielkiej Brytanii i Włoch. Zastosowano systematyczny przegląd literatury w celu zbadania zagadnienia udziału osób starszych w badaniach klinicznych, czynników sprzyjających ich uczestnictwu i utrudniających to uczestnictwo, przyczyn niskiego uczestnictwa oraz sposobów jego zwiększania. Wyniki. Potwierdzono hipotezę małej i nierównej reprezentacji osób starszych w badaniach klinicznych, a wyniki przeglądu stały się podstawą do przeprowadzenia w 9 krajach badań opinii pracowników opieki zdrowotnej oraz opinii pacjentów w starszym wieku na temat udziału osób starszych w badaniach klinicznych. Wnioski. Ostatecznym rezultatem tych badań jest karta zawierająca rekomendacje zmierzające do zapewnienia równoprawnego udziału osób starszych w badaniach klinicznych.Background. Several research reports indicate that elderly persons are underrepresented in the clinical trials on which clinical recommendations are based. This gave stimulus to perform the ‘Increasing the PaRticipation of the ElDerly In Clinical Trials’ (PREDICT) project, financed by the EU within the FP7. The goal of the PREDICT was to establish the reasons and extent to which old people are excluded from trials based on age-related criteria. Material and methods. The project gathered investigators from 11 institutions in 9 countries: Czech Republic, Israel, Italy, Lithuania, the Netherlands, Poland, Romania, Spain, and the UK. The systematic review of literature has been applied to assess the scope of the problem in terms of participation, predisposing and obstructive factors, reasons of low participation and possible interventions to enhance it. Results. The hypothesis of low and unequal representation of older people in clinical research has been confirmed. The systematic review results became the background for conducting in 9 countries a study of opinion shared by the health care professionals and elderly patients on their participation in clinical research. Conclusions. The analysis of gathered data enabled creation of PREDICT charter which contains recommendations aiming to assure the equal rights to older people to participate in clinical trials

Atlas of lesion locations and postsurgical seizure freedom in focal cortical dysplasia: A MELD study.

Funder: National Institute for Health Research (NIHR) GOSH BRCOBJECTIVE: Drug-resistant focal epilepsy is often caused by focal cortical dysplasias (FCDs). The distribution of these lesions across the cerebral cortex and the impact of lesion location on clinical presentation and surgical outcome are largely unknown. We created a neuroimaging cohort of patients with individually mapped FCDs to determine factors associated with lesion location and predictors of postsurgical outcome. METHODS: The MELD (Multi-centre Epilepsy Lesion Detection) project collated a retrospective cohort of 580 patients with epilepsy attributed to FCD from 20 epilepsy centers worldwide. Magnetic resonance imaging-based maps of individual FCDs with accompanying demographic, clinical, and surgical information were collected. We mapped the distribution of FCDs, examined for associations between clinical factors and lesion location, and developed a predictive model of postsurgical seizure freedom. RESULTS: FCDs were nonuniformly distributed, concentrating in the superior frontal sulcus, frontal pole, and temporal pole. Epilepsy onset was typically before the age of 10 years. Earlier epilepsy onset was associated with lesions in primary sensory areas, whereas later epilepsy onset was associated with lesions in association cortices. Lesions in temporal and occipital lobes tended to be larger than frontal lobe lesions. Seizure freedom rates varied with FCD location, from around 30% in visual, motor, and premotor areas to 75% in superior temporal and frontal gyri. The predictive model of postsurgical seizure freedom had a positive predictive value of 70% and negative predictive value of 61%. SIGNIFICANCE: FCD location is an important determinant of its size, the age at epilepsy onset, and the likelihood of seizure freedom postsurgery. Our atlas of lesion locations can be used to guide the radiological search for subtle lesions in individual patients. Our atlas of regional seizure freedom rates and associated predictive model can be used to estimate individual likelihoods of postsurgical seizure freedom. Data-driven atlases and predictive models are essential for evidence-based, precision medicine and risk counseling in epilepsy