The balance of power: accretion and feedback in stellar mass black holes

In this review we discuss the population of stellar-mass black holes in our galaxy and beyond, which are the extreme endpoints of massive star evolution. In particular we focus on how we can attempt to balance the available accretion energy with feedback to the environment via radiation, jets and winds, considering also possible contributions to the energy balance from black hole spin and advection. We review quantitatively the methods which are used to estimate these quantities, regardless of the details of the astrophysics close to the black hole. Once these methods have been outlined, we work through an outburst of a black hole X-ray binary system, estimating the flow of mass and energy through the different accretion rates and states. While we focus on feedback from stellar mass black holes in X-ray binary systems, we also consider the applicability of what we have learned to supermassive black holes in active galactic nuclei. As an important control sample we also review the coupling between accretion and feedback in neutron stars, and show that it is very similar to that observed in black holes, which strongly constrains how much of the astrophysics of feedback can be unique to black holes.Comment: To be published in Haardt et al. Astrophysical Black Holes. Lecture Notes in Physics. Springer 201

InterMEL: An international biorepository and clinical database to uncover predictors of survival in early-stage melanoma

INTRODUCTION: We are conducting a multicenter study to identify classifiers predictive of disease-specific survival in patients with primary melanomas. Here we delineate the unique aspects, challenges, and best practices for optimizing a study of generally small-sized pigmented tumor samples including primary melanomas of at least 1.05mm from AJTCC TNM stage IIA-IIID patients. We also evaluated tissue-derived predictors of extracted nucleic acids' quality and success in downstream testing. This ongoing study will target 1,000 melanomas within the international InterMEL consortium. METHODS: Following a pre-established protocol, participating centers ship formalin-fixed paraffin embedded (FFPE) tissue sections to Memorial Sloan Kettering Cancer Center for the centralized handling, dermatopathology review and histology-guided coextraction of RNA and DNA. Samples are distributed for evaluation of somatic mutations using next gen sequencing (NGS) with the MSK-IMPACTTM assay, methylation-profiling (Infinium MethylationEPIC arrays), and miRNA expression (Nanostring nCounter Human v3 miRNA Expression Assay). RESULTS: Sufficient material was obtained for screening of miRNA expression in 683/685 (99%) eligible melanomas, methylation in 467 (68%), and somatic mutations in 560 (82%). In 446/685 (65%) cases, aliquots of RNA/DNA were sufficient for testing with all three platforms. Among samples evaluated by the time of this analysis, the mean NGS coverage was 249x, 59 (18.6%) samples had coverage below 100x, and 41/414 (10%) failed methylation QC due to low intensity probes or insufficient Meta-Mixed Interquartile (BMIQ)- and single sample (ss)- Noob normalizations. Six of 683 RNAs (1%) failed Nanostring QC due to the low proportion of probes above the minimum threshold. Age of the FFPE tissue blocks (p<0.001) and time elapsed from sectioning to co-extraction (p = 0.002) were associated with methylation screening failures. Melanin reduced the ability to amplify fragments of 200bp or greater (absent/lightly pigmented vs heavily pigmented, p<0.003). Conversely, heavily pigmented tumors rendered greater amounts of RNA (p<0.001), and of RNA above 200 nucleotides (p<0.001). CONCLUSION: Our experience with many archival tissues demonstrates that with careful management of tissue processing and quality control it is possible to conduct multi-omic studies in a complex multi-institutional setting for investigations involving minute quantities of FFPE tumors, as in studies of early-stage melanoma. The study describes, for the first time, the optimal strategy for obtaining archival and limited tumor tissue, the characteristics of the nucleic acids co-extracted from a unique cell lysate, and success rate in downstream applications. In addition, our findings provide an estimate of the anticipated attrition that will guide other large multicenter research and consortia

Influence of sweetpotato rooting characteristics on infestation and damage by Cylas spp

Studies were carried out in the field at Serere Agricultural and Animal Production Research Institute (SAARI), Eastern Uganda, to establish whether the existing sweetpotato germplasm in Uganda has cultivars resistant to the sweetpotato weevils, Cylas spp. The trials were conducted during the two growing seasons of 1997. Root size was the only sweetpotato rooting characteristic that significantly influenced tuber infestation (P=0.009) and damage (P=0.049). Root size was positively correlated to tuber infestation by Cylas spp. (Y=0.0456x + 21.206; R2 = 0.2731) and negatively correlated to damage by Cylas weevils (Y=-0.027x + 29.684, R2=0.1647). A laboratory study demonstrated the effect of temperature on oviposition, survival and developement of Cylas puncticollis (Boheman). The variety 'Tanzania' that was used as the susceptible check registered the highest weevil emergence under both wet and dry weather conditions while varieties 'Kasira' and 'Akere-Ikokolak' registered the least emergence of adult C. puncticollis. These results indicate that the latter two varieties posses considerable levels of resistance to sweetpotato weevils. Key Words: Germplasm, resistance, sweetpotato weevils, Uganda (African Crop Science Journal 2001 9(1): 165-174

Predicting pain and function outcomes in people consulting with shoulder pain:The PANDA-S clinical cohort and qualitative study protocol (ISRCTN 46948079)

IntroductionShoulder pain is common in primary care but achieving definitive diagnosis is contentious leading to uncertainty in management. To inform optimal primary care for patients with shoulder pain, the study aims to (i) to investigate the short- and long-term outcomes (overall prognosis) of shoulder pain, (ii) estimate costs of care, (iii) develop a prognostic model for predicting individuals’ level and risk of pain and disability at 6 months, (iv) investigate experiences and opinions of patients and healthcare professionals regarding diagnosis, prognosis, and management of shoulder pain.Methods and analysisPANDA-S is a longitudinal clinical cohort with linked qualitative study. At least 400 people presenting to general practice and physiotherapy services in the UK will be recruited. Participants will complete questionnaires at baseline, 3, 6, 12, 24 and 36 months. Short-term data will be collected weekly between baseline and 12 weeks via SMS text or software application (App). Participants will be offered clinical (physiotherapist) and ultrasound (sonographer) assessments at baseline. Qualitative interviews with ≈15 dyads of patients and their healthcare professional (GP or physiotherapist). Short and long-term trajectories of shoulder pain and disability (using SPADI) will be described, using latent class growth analysis. Health economic analysis will estimate direct costs of care and indirect costs related to work absence and productivity losses. Multivariableregression analysis will be used to develop a prognostic model predicting future levels of pain and disability at 6-months using penalisation methods to adjust for overfitting. The added predictive value of pre-specified physical examination tests and ultrasound findings will be examined. For the qualitative interviews an inductive, exploratory framework will be adopted using thematic analysis to investigate decision making and perspectives of patients and clinicians on the importance of diagnostic and prognostic information when negotiatingtreatment and referral options