Speeding up ecological and evolutionary computations in R; essentials of high performance computing for biologists

Computation has become a critical component of research in biology. A risk has emerged that computational and programming challenges may limit research scope, depth, and quality. We review various solutions to common computational efficiency problems in ecological and evolutionary research. Our review pulls together material that is currently scattered across many sources and emphasizes those techniques that are especially effective for typical ecological and environmental problems. We demonstrate how straightforward it can be to write efficient code and implement techniques such as profiling or parallel computing. We supply a newly developed R package (aprof) that helps to identify computational bottlenecks in R code and determine whether optimization can be effective. Our review is complemented by a practical set of examples and detailed Supporting Information material (S1–S3 Texts) that demonstrate large improvements in computational speed (ranging from 10.5 times to 14,000 times faster). By improving computational efficiency, biologists can feasibly solve more complex tasks, ask more ambitious questions, and include more sophisticated analyses in their research

Subphenotypes in acute kidney injury : a narrative review

Acute kidney injury (AKI) is a frequently encountered syndrome especially among the critically ill. Current diagnosis of AKI is based on acute deterioration of kidney function, indicated by an increase in creatinine and/or reduced urine output. However, this syndromic definition encompasses a wide variety of distinct clinical features, varying pathophysiology, etiology and risk factors, and finally very different short- and long-term outcomes. Lumping all AKI together may conceal unique pathophysiologic processes specific to certain AKI populations, and discovering these AKI subphenotypes might help to develop targeted therapies tackling unique pathophysiological processes. In this review, we discuss the concept of AKI subphenotypes, current knowledge regarding both clinical and biomarker-driven subphenotypes, interplay with AKI subphenotypes and other ICU syndromes, and potential future and clinical implications.Peer reviewe

Subphenotypes in acute kidney injury : a narrative review

Acute kidney injury (AKI) is a frequently encountered syndrome especially among the critically ill. Current diagnosis of AKI is based on acute deterioration of kidney function, indicated by an increase in creatinine and/or reduced urine output. However, this syndromic definition encompasses a wide variety of distinct clinical features, varying pathophysiology, etiology and risk factors, and finally very different short- and long-term outcomes. Lumping all AKI together may conceal unique pathophysiologic processes specific to certain AKI populations, and discovering these AKI subphenotypes might help to develop targeted therapies tackling unique pathophysiological processes. In this review, we discuss the concept of AKI subphenotypes, current knowledge regarding both clinical and biomarker-driven subphenotypes, interplay with AKI subphenotypes and other ICU syndromes, and potential future and clinical implications.Peer reviewe

Detection of reduced carbon in a basalt analogue for martian nakhlite : a signpost to habitat on Mars

C. W. Taylor and J. Still are thanked for skilled technical support. J. Parnell, H.G.M. Edwards, I. Hutchinson and R. Ingley acknowledge the support of the UKSA and the STFC Research Council in the UK ExoMars programme. L. V. Harris and S. McMahon acknowledge STFC studentship funding.Peer reviewedPublisher PD

(6S)-2,4-Di-tert-butyl-6-[(4S,5R)-3-iso­propyl-4-methyl-5-phenyloxazolidin-2-yl]phenol

The title oxazolidine compound, C27H39NO2, was synthesized from N-isopropyl­norephedrine. The dihedral angle between the aromatic rings is 70.33 (5)°. The N atom of the heterocycle is oriented to allow intra­molecular O—H⋯N hydrogen bonding with the hydr­oxy substituent

Contemporary visions of progress in ecology and thoughts for the future

Although ecological research is progressing rapidly, the answers to certain key questions continue to elude us. This paper considers several of the contemporary challenges facing ecology. (1) Terminology is voluminous and often poorly defined, resulting in inefficient communication. (2) The concept of scale affects our inferences about system structure and function, requiring us to continue an almost heuristic investigation of breaks, domains, and integration. New tools that more explicitly incorporate scalar issues will need to be developed for progress to take place in the field of ecology. (3) Increasingly, it is expected that applied questions will be solved in less than a year. This demand for solutions from ecologists often produces short-term and inadequate responses. (4) How can ecologists improve communication between subdisciplines, with undergraduate students, and with the public? How will ecology be done in the future, and by whom? We provide some background to these observations and questions, and offer some potential solutions from the viewpoint of young practicing ecologists

A laboratory for multi-century science

Charles Cockell and colleagues consider what it takes to establish and maintain an experiment that lasts for decades – or even for centuries

Design of 280 GHz feedhorn-coupled TES arrays for the balloon-borne polarimeter SPIDER

We describe 280 GHz bolometric detector arrays that instrument the balloon-borne polarimeter SPIDER. A primary science goal of SPIDER is to measure the large-scale B-mode polarization of the cosmic microwave background in search of the cosmic-inflation, gravitational-wave signature. 280 GHz channels aid this science goal by constraining the level of B-mode contamination from galactic dust emission. We present the focal plane unit design, which consists of a 16$\times$16 array of conical, corrugated feedhorns coupled to a monolithic detector array fabricated on a 150 mm diameter silicon wafer. Detector arrays are capable of polarimetric sensing via waveguide probe-coupling to a multiplexed array of transition-edge-sensor (TES) bolometers. The SPIDER receiver has three focal plane units at 280 GHz, which in total contains 765 spatial pixels and 1,530 polarization sensitive bolometers. By fabrication and measurement of single feedhorns, we demonstrate 14.7$^{\circ}$ FHWM Gaussian-shaped beams with $<$1% ellipticity in a 30% fractional bandwidth centered at 280 GHz. We present electromagnetic simulations of the detection circuit, which show 94% band-averaged, single-polarization coupling efficiency, 3% reflection and 3% radiative loss. Lastly, we demonstrate a low thermal conductance bolometer, which is well-described by a simple TES model and exhibits an electrical noise equivalent power (NEP) = 2.6 $\times$ 10$^{-17}$ W/$\sqrt{\mathrm{Hz}}$, consistent with the phonon noise prediction.Comment: Proceedings of SPIE Astronomical Telescopes + Instrumentation 201