PinAPL-Py: A comprehensive web-application for the analysis of CRISPR/Cas9 screens.

Large-scale genetic screens using CRISPR/Cas9 technology have emerged as a major tool for functional genomics. With its increased popularity, experimental biologists frequently acquire large sequencing datasets for which they often do not have an easy analysis option. While a few bioinformatic tools have been developed for this purpose, their utility is still hindered either due to limited functionality or the requirement of bioinformatic expertise. To make sequencing data analysis of CRISPR/Cas9 screens more accessible to a wide range of scientists, we developed a Platform-independent Analysis of Pooled Screens using Python (PinAPL-Py), which is operated as an intuitive web-service. PinAPL-Py implements state-of-the-art tools and statistical models, assembled in a comprehensive workflow covering sequence quality control, automated sgRNA sequence extraction, alignment, sgRNA enrichment/depletion analysis and gene ranking. The workflow is set up to use a variety of popular sgRNA libraries as well as custom libraries that can be easily uploaded. Various analysis options are offered, suitable to analyze a large variety of CRISPR/Cas9 screening experiments. Analysis output includes ranked lists of sgRNAs and genes, and publication-ready plots. PinAPL-Py helps to advance genome-wide screening efforts by combining comprehensive functionality with user-friendly implementation. PinAPL-Py is freely accessible at http://pinapl-py.ucsd.edu with instructions and test datasets

The developmental environment modulates mating-induced aggression and fighting success in adult female Drosophila

Funding Information Rhodes Trust Brazilian Research Council. Grant Number: 211668/2013‐3 St. John's College, University of Oxford Christ Church College, University of Oxford Biotechnology and Biological Sciences Research Council. Grant Number: BB/K014544/1Peer reviewedPublisher PD

DNA as a universal substrate for chemical kinetics

Molecular programming aims to systematically engineer molecular and chemical systems of autonomous function and ever-increasing complexity. A key goal is to develop embedded control circuitry within a chemical system to direct molecular events. Here we show that systems of DNA molecules can be constructed that closely approximate the dynamic behavior of arbitrary systems of coupled chemical reactions. By using strand displacement reactions as a primitive, we construct reaction cascades with effectively unimolecular and bimolecular kinetics. Our construction allows individual reactions to be coupled in arbitrary ways such that reactants can participate in multiple reactions simultaneously, reproducing the desired dynamical properties. Thus arbitrary systems of chemical equations can be compiled into real chemical systems. We illustrate our method on the Lotka–Volterra oscillator, a limit-cycle oscillator, a chaotic system, and systems implementing feedback digital logic and algorithmic behavior

Glyceryl trinitrate for the treatment of ischaemic stroke: Determining efficacy in rodent and ovine species for enhanced clinical translation

Hypertension is a leading risk factor for death and dependency after ischaemic stroke. However, administering anti-hypertensive medications post-stroke remains contentious with concerns regarding deleterious effects on cerebral blood flow and infarct expansion. This study sought to determine the effect of glyceryl trinitrate (GTN) treatment in both lissencephalic and gyrencephalic pre-clinical stroke models. Merino sheep underwent middle cerebral artery occlusion (MCAO) followed by GTN or control patch administration (0.2 mg/h). Monitoring of numerous physiologically relevant measures over 24 h showed that GTN administration was associated with decreased intracranial pressure, infarct volume, cerebral oedema and midline shift compared to vehicle treatment (p ≤ 0.05). No significant changes in blood pressure or cerebral perfusion pressure were observed. Using optical imaging spectroscopy and laser speckle imaging, the effect of varying doses of GTN (0.69–50 µg/h) on cerebral blood flow and tissue oxygenation was examined in mice. No consistent effect was found. Additional mice undergoing MCAO followed by GTN administration (doses varying from 0–60 µg/h) also showed no improvement in infarct volume or neurological score within 24 h post-stroke. GTN administration significantly improved numerous stroke-related physiological outcomes in sheep but was ineffective in mice. This suggests that, whilst GTN administration could potentially benefit patients, further research into mechanisms of action are required

Central adjudication of serious adverse events did not affect trial's safety results: Data from the Efficacy of Nitric Oxide in Stroke (ENOS) trial

Background and purpose Central adjudication of serious adverse events (SAEs) can be undertaken in clinical trials, especially for open-label studies where outcome assessment may be at risk of bias. This study explored the effect of central adjudication of SAEs on the safety results of the Efficacy of Nitric Oxide in Stroke (ENOS) Trial. Methods ENOS assigned patients with acute stroke at random to receive either transdermal glyceryl trinitrate (GTN) or no GTN and to Stop or Continue previous antihypertensive treatment. SAEs were reported by local investigators who were not blinded to treatment allocation. Central adjudicators, blinded to treatment allocation, reviewed the investigators reports and used evidence available to confirm or re-categorise the classification of event, likely causality, diagnosis and expectedness of event. Results Of 4011 patients enrolled in ENOS, 1473 SAEs were reported by local investigators; this was reduced to 1444 after the review by adjudicators, with 29 re-classified as not an SAE. There was fair agreement between investigators and adjudicators regarding likely causality, with 808 agreements and 644 disagreements (56% crude agreement, weighted kappa, κ = 0.31). Agreement increased upon dichotomisation of the causality categories, with 1432 agreements and 20 disagreements (99% crude agreement, kappa = 0.54). Repeating the main trial safety analysis with investigator reported events showed that adjudication had no effect on the main trial safety conclusions. Conclusions In a large trial, with many SAEs reported, central adjudication of these events did not affect trial conclusions. This suggests that adjudication of SAEs in a clinical trial where the intervention already has a well-established safety profile may not be necessary. Potential efficiency savings (financial, logistical) can be made through not adjudicating SAEs

Evaluating the effectiveness of agricultural adaptation to climate change in preindustrial society

The effectiveness of agricultural adaptation determines the vulnerability of this sector to climate change, particularly during the preindustrial era. However, this effectiveness has rarely been quantitatively evaluated, specifically at a large spatial and long-term scale. The present study covers this case of preindustrial society in AD 1500–1800. Given the absence of technological innovations in this time frame, agricultural production was chiefly augmented by cultivating more land (land input) and increasing labor input per land unit (labor input). Accordingly, these two methods are quantitatively examined. Statistical results show that within the study scale, land input is a more effective approach of mitigating climatic impact than labor input. Nonetheless, these observations collectively improve Boserup's theory from the perspective of a large spatial and long-term scale.postprin

The pirate in the pump: children's views of objects as imaginary friends at the start of school

The main aim of this paper is to use a phenomenological approach (Merleau-Ponty, 1962. Phenomenology of Perception. Evanston: Northwestern University Press; Merleau-Ponty. 1968. The Visible and the Invisible: Followed by Working Notes. Evanston: Northern University Press) to contribute a new theoretical understanding of what imaginary friends mean for children in the context of starting school. The paper addresses the specific area of ‘object-friends’ and draws on examples from an empirical and consultative study of a small sample of five and six-year-old children’s everyday experiences of friendship in school. The paper argues that if practitioners consider embodiment approaches and listen attentively to the knowledge and information that children share about their imaginary friends, this could be used to nurture children’s early learnin

Climate and society in long-term perspective: opportunities and pitfalls in the use of historical datasets

Recent advances in palaeoclimatology and the growing digital availability of large historical datasets on human activity have created new opportunities to investigate long-term interactions between climate and society. However, noncritical use of historical datasets can create pitfalls, resulting in misleading findings that may become entrenched as accepted knowledge. We demonstrate pitfalls in the content, use and interpretation of historical datasets in research into climate and society interaction through a systematic review of recent studies on the link between climate and (a) conflict incidence, (b) plague outbreaks and (c) agricultural productivity changes. We propose three sets of interventions to overcome these pitfalls, which involve a more critical and multidisciplinary collection and construction of historical datasets, increased specificity and transparency about uncertainty or biases, and replacing inductive with deductive approaches to causality. This will improve the validity and robustness of interpretations on the long-term relationship between climate and society