Generating optimized Fourier interpolation routines for density function theory using SPIRAL

© 2015 IEEE.Upsampling of a multi-dimensional data-set is an operation with wide application in image processing and quantum mechanical calculations using density functional theory. For small up sampling factors as seen in the quantum chemistry code ONETEP, a time-shift based implementation that shifts samples by a fraction of the original grid spacing to fill in the intermediate values using a frequency domain Fourier property can be a good choice. Readily available highly optimized multidimensional FFT implementations are leveraged at the expense of extra passes through the entire working set. In this paper we present an optimized variant of the time-shift based up sampling. Since ONETEP handles threading, we address the memory hierarchy and SIMD vectorization, and focus on problem dimensions relevant for ONETEP. We present a formalization of this operation within the SPIRAL framework and demonstrate auto-generated and auto-tuned interpolation libraries. We compare the performance of our generated code against the previous best implementations using highly optimized FFT libraries (FFTW and MKL). We demonstrate speed-ups in isolation averaging 3x and within ONETEP of up to 15%

The Value of Comparative Animal Research : Krogh’s Principle Facilitates Scientific Discoveries

There are no conflicts of interest to declare. This paper developed from the 2016 Early Career Impact Award from the Federation of Associations in Behavioral & Brain Sciences to TJS. TJS has received funding from The Leverhulme Trust. FJPE is in receipt of funding from the BBSRC (BB/M001555/1). The National Institutes of Health has funded RDF (NS 034950, NS093277, NIMH 087930), AGO (HD079573, IOS-1354760) and AMK (HD081959). BAA is an Arnold O. Beckman postdoctoral fellow.Peer reviewedPostprin

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics.

BackgroundSingle-cell transcriptomics allows researchers to investigate complex communities of heterogeneous cells. It can be applied to stem cells and their descendants in order to chart the progression from multipotent progenitors to fully differentiated cells. While a variety of statistical and computational methods have been proposed for inferring cell lineages, the problem of accurately characterizing multiple branching lineages remains difficult to solve.ResultsWe introduce Slingshot, a novel method for inferring cell lineages and pseudotimes from single-cell gene expression data. In previously published datasets, Slingshot correctly identifies the biological signal for one to three branching trajectories. Additionally, our simulation study shows that Slingshot infers more accurate pseudotimes than other leading methods.ConclusionsSlingshot is a uniquely robust and flexible tool which combines the highly stable techniques necessary for noisy single-cell data with the ability to identify multiple trajectories. Accurate lineage inference is a critical step in the identification of dynamic temporal gene expression

The association of attention deficit hyperactivity disorder with socioeconomic disadvantage: alternative explanations and evidence

addresses: ESRC Centre for Genomics in Society (Egenis) & Institute of Health Research, University of Exeter Medical School, Exeter, UK.OnlineOpen Article. This is a copy of an article published in the Journal of Child Psychology and Psychiatry. This journal is available online at: http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1469-7610Studies throughout Northern Europe, the United States and Australia have found an association between childhood attention deficit hyperactivity disorder (ADHD) and family socioeconomic disadvantage. We report further evidence for the association and review potential causal pathways that might explain the link.ESRC’s Secondary Data Analysis InitiativeNational Institute for Health Research (NIHR) Collaboration for Leadership in Applied Health Research and Care (CLAHRC) for the South West Peninsul

Effects of a Triphasic Block Method on Power in Collegiate Basketball Players

Implementing a non-traditional method for a training cycle may serve as an alternative means of developing maximal strength and power. Seven male Division I intercollegiate basketball players (age=21.0±0.63 yrs, ht=191.86±7.24cm, wt=94.8±14.9kg, training experience = 2.2 ± 1.3 yrs) who recently completed a 5-month competitive season were recruited for this study. The testing took place during the off-season, when the players were not involved in NCAA competition. Subjects underwent a three-week preparation phase, followed by a pre-test vertical jump (CMJ), standing broad jump (SBJ), and back squat 1-repetition max (1RM). Prior to all testing sessions, the participants participated in a dynamic warm-up, and were allowed to familiarize themselves with each test. The training methods were developed as three, two-week phases, with the triphasic and plyometric methods included “French contrast training” along with the barbell back squat (BBS). The first phase had an eccentric emphasis, the second phase an isometric emphasis, and the third phase had a concentric emphasis. With the respective phase, the contraction emphasis was applied to the BBS, either completing 6-second eccentric portions, 3-second isometric portions, or dynamic concentric portions of the exercise. Each set was followed by a series of both reactive plyometrics, followed by resisted plyometrics. The triphasic emphasis was rotated throughout a 6-week period. At the end of six weeks, the participants had a recovery week, then underwent post-testing. Data was analyzed between the pre-test and post-test CMJ, SBJ and 1RM. There was a significant difference between CMJ improvement following a Triphasic Block Method (TBM) vs. a traditional method of training (