SHAPE selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data

Selective 2′ Hydroxyl Acylation analyzed by Primer Extension (SHAPE) is an accurate method for probing of RNA secondary structure. In existing SHAPE methods, the SHAPE probing signal is normalized to a no-reagent control to correct for the background caused by premature termination of the reverse transcriptase. Here, we introduce a SHAPE Selection (SHAPES) reagent, N-propanone isatoic anhydride (NPIA), which retains the ability of SHAPE reagents to accurately probe RNA structure, but also allows covalent coupling between the SHAPES reagent and a biotin molecule. We demonstrate that SHAPES-based selection of cDNA–RNA hybrids on streptavidin beads effectively removes the large majority of background signal present in SHAPE probing data and that sequencing-based SHAPES data contain the same amount of RNA structure data as regular sequencing-based SHAPE data obtained through normalization to a no-reagent control. Moreover, the selection efficiently enriches for probed RNAs, suggesting that the SHAPES strategy will be useful for applications with high-background and low-probing signal such as in vivo RNA structure probing

Group-based exercise in daily clinical practice to improve physical fitness in men with prostate cancer undergoing androgen deprivation therapy:study protocol

INTRODUCTION: Level 1 evidence supports the use of supervised exercise to mitigate the adverse effects of androgen deprivation therapy (ADT) in men with prostate cancer. The data, however, have been generated in controlled research settings and might not be transferable to daily clinical practice. This article describes the design of an ongoing prospective observational study to evaluate the potential benefits of exercise in daily clinical practice. METHODS AND ANALYSIS: Men diagnosed with prostate cancer starting or already receiving ADT at our facility are invited to participate in a 12-week exercise programme implemented as the standard of care. Exclusion criteria are opioid-demanding treatment for skeletal pain, an Eastern Cooperative Oncology Group (ECOG) performance status above 2 or the inability to perform floor and machine exercises independently. The intervention consists of an initial educational session of 1½ hours followed by 12 weeks of group-based supervised training two times a week. The focus of the exercise is progressive resistance training in combination with aerobic training. Participants are measured at baseline, after 12 weeks and after 24 weeks as part of the programme. Primary endpoints of this study are changes in physical fitness evaluated by the 30 s Chair-Stand Test and Graded Cycling Test with Talk Test. Secondary endpoints include changes in quality of life, body composition and safety of exercise. Inclusion started in August 2014, with 169 participants being included by December 2015. ETHICS AND DISSEMINATION: The study has been reviewed by the Scientific Ethical Committee of the Capital Region of Denmark (reference number H-3-2013-FSP39). The results of the study will be published in peer-reviewed international journals and will be presented at national and international conferences and symposiums. TRIAL REGISTRATION NUMBER: NCT02631681; Pre-results

What Does It Take for Research to Be Rehabilitation Research?

Six recommendations to facilitate rehabilitation research and supplement existing research practices were identified. Rehabilitation practice requires research addressing different long-term multi-faceted needs and perspectives of end users, including service users, professionals, politicians, and administrators. Research in rehabilitation should therefore integrate different research traditions and methods. Rehabilitation research with a broad focus is sparse, and most of the research takes its starting point in the biomedical research tradition. Through a nominal group process, we developed recommendations to emphasize important issues in rehabilitation research

Bubble observations and analysis of the Renland ice core

Bubbles in ice cores store various information about climate conditions during densification and pore close-off in former times. Very recently it was shown that bubbles can additionally be used as marker for cumulated strain within the ice. Bubble studies on the Renland ice core are from particular interest: the Renland ice core includes the oldest bubbly ice retrieved so far in ice core drilling projects and it contains bubbly ice that has been exposed to tremendous deformation and thinning. The Renland ice core of 584 m length was drilled through the ice cap during May-June 2015 in the framework of RECAP (Renland ice cap drilling project). The ice shows no clathrate formation. Preliminary considerations suggest Holocene and Glacial ice with Eemian ice close to bedrock. Core sections of the Renland ice core from selected depth intervals are measured with the means of X-ray computer tomography using the core-scale AWI-ICE CT. The measurements are performed with a spatial resolution of 15µm and provide 3d- bubble arrangements. Different bubble shape factors, bubble volume (porosity), bubble centre distributions and bubble next neighbor functions are derived. We present first depth profiles of these parameters and discuss the results in context of deformation mechanism and paleo climate. It will contribute to reconstruct the complex deformation history of the Renland ice cap