Training Big Random Forests with Little Resources

Without access to large compute clusters, building random forests on large datasets is still a challenging problem. This is, in particular, the case if fully-grown trees are desired. We propose a simple yet effective framework that allows to efficiently construct ensembles of huge trees for hundreds of millions or even billions of training instances using a cheap desktop computer with commodity hardware. The basic idea is to consider a multi-level construction scheme, which builds top trees for small random subsets of the available data and which subsequently distributes all training instances to the top trees' leaves for further processing. While being conceptually simple, the overall efficiency crucially depends on the particular implementation of the different phases. The practical merits of our approach are demonstrated using dense datasets with hundreds of millions of training instances.Comment: 9 pages, 9 Figure

The lactation cycle of the fur seal

The fur seal is a mammal with an unusual ability to turn its milk production on and off without significantly altering the gross morphology of the mammary gland. This atypical lactation cycle is due to the fact that maternal foraging and infant nursing are spatially and temporally separate (Bonner, 1984). Maternal care involves the suckling of offspring over a period of at least 4 months, but lactation can extend to more than 12 months. Following a perinatal fast of approximately 1 week, females depart the breeding colony to forage at sea and, for the remainder of lactation, alternate between short periods ashore suckling their young with longer periods of up to 4 weeks foraging at sea. Whilst foraging at sea, milk production in the fur seal mammary gland either ceases or is reduced (Arnould &amp; Boyd, 1995b).<br /

A biomechanical analysis of the stand-up paddle board stroke: A comparative study

Background: Stand-up paddle boarding (SUP) is a rapidly growing global aquatic sport, with increasing popularity among participants within recreation, competition and rehabilitation. To date, few scientific studies have focused on SUP. Further, there is no research examining the biomechanics of the SUP paddle stroke. The purpose of this study was to investigate whether variations in kinematics existed among experienced and inexperienced SUP participants using three-dimensional motion analysis. This data could be of significance to participants, researchers, coaches and health practitioners to improve performance and inform injury minimization strategies. Methods: A cross-sectional observational design study was performed with seven experienced and 19 inexperienced paddlers whereby whole-body kinematic data were acquired using a six-camera Vicon motion capture system. Participants paddled on a SUP ergometer while three-dimensional range of motion (ROM) and peak joint angles were calculated for the shoulders, elbows, hips and trunk. Mann-Whitney U tests were conducted on the non-normally distributed data to evaluate differences between level of expertise. Results: Significant differences in joint kinematics were found between experienced and inexperienced participants, with inexperienced participants using greater overall shoulder ROM (78.9° ± 24.9° vs 56.6° ± 17.3°, p = 0.010) and less hip ROM than the experienced participants (50.0° ± 18.5° vs 66.4° ± 11.8°, p = 0.035). Experienced participants demonstrated increased shoulder motion at the end of the paddle stoke compared to the inexperienced participants (74.9° ± 16.3° vs 35.2° ± 28.5°, p = 0.001 minimum shoulder flexion) and more extension at the elbow (6.0° ± 9.2° minimum elbow flexion vs 24.8° ± 13.5°, p = 0.000) than the inexperienced participants. Discussion: The results of this study indicate several significant kinematic differences between the experienced and inexperienced SUP participants. These variations in technique were noted in the shoulder, elbow and hip and are evident in other aquatic paddling sports where injury rates are higher in these joints. These finding may be valuable for coaches, therapists and participants needing to maximize performance and minimize injury risk during participation in SUP.Full Tex

The Dependence of Brown Dwarf Radii on Atmospheric Metallicity and Clouds: Theory and Comparison with Observations

Employing realistic and consistent atmosphere boundary conditions, we have generated evolutionary models for brown dwarfs and very-low-mass stars (VLMs) for different metallicities ([Fe/H]), with and without clouds. We find that the spread in radius at a given mass and age can be as large as $\sim$10% to $\sim$25%, with higher-metallicity, higher-cloud-thickness atmospheres resulting quite naturally in larger radii. For each 0.1 dex increase in [Fe/H], radii increase by $\sim$1% to $\sim$2.5%, depending upon age and mass. We also find that, while for smaller masses and older ages brown dwarf radii decrease with increasing helium fraction ($Y$) (as expected), for more massive brown dwarfs and a wide range of ages they increase with helium fraction. The increase in radius in going from $Y=0.25$ to $Y=0.28$ can be as large as $\sim$0.025 \rj\ ($\sim$2.5%). Furthermore, we find that for VLMs an increase in atmospheric metallicity from 0.0 to 0.5 dex, increases radii by $\sim$4%, and from -0.5 to 0.5 dex by $\sim$10%. Therefore, we suggest that opacity due to higher metallicity might naturally account for the apparent radius anomalies in some eclipsing VLM systems. Ten to twenty-five percent variations in radius exceed errors stemming from uncertainities in the equation of state alone. This serves to emphasize that transit and eclipse measurements of brown dwarf radii constrain numerous effects collectively, importantly including the atmosphere and condensate cloud models, and not just the equation of state. At all times, one is testing a multi-parameter theory, and not a universal radius$-$mass relation.Comment: Accepted to the Astrophysical Journal, May 3, 201

MammoSapiens: eResearch of the lactation program. Building online facilities for collaborative molecular and evolutionary analysis of lactation and other biological systems from gene sequences and gene expression data.

Delivering bioinformatics power to life science researchers inevitably runs into problems of limited computing resources in the context of exponentially increasing data sources, access time, costs, lack of skills and, rapidly evolving technology and software tools with poorly defined standards. In this context the development of online facilities to best enable collaborative research often needs to be customized to specific project applications in close cooperation with the experimentalist users and, to be concerned with the storage and management of results to allow more consistency and traceability of results on a broad access data mining platform. Here we showcase an Internet based research platform using the PHP/MySQL paradigm for the collaborative, integrative and comparative analysis of lactation related gene sequences and gene expression experiments to support lactation research. We also illustrate how these resources are used, how they enable research by allowing meta-analysis of data and results and, how the bottom-up development of customized eResearch components can lead to the production of more generic functional software tools and eResearch environments for deployment to a larger number of biological researchers working on other bio-systems

Dicer loss and recovery induce an oncogenic switch driven by transcriptional activation of the oncofetal Imp1–3 family

MicroRNAs(miRNAs) are post-transcriptional regulators of gene expressioncritical for organismal viability. Changes inmiRNAactivity arecommonin cancer, buthowthese changes relate to subsequent alterations in transcription and the process of tumorigenesis is not well understood. Here, we report a deep transcriptional, oncogenic network regulated bymiRNAs. Wepresent analysis of the gene expression and phenotypic changes associated with globalmiRNA restoration in miRNA-deficient fibroblasts. This analysis uncovers a miRNA-repressed network containing oncofetal genesImp1, Imp2, and Imp3(Imp1–3) that is up-regulated primarily transcriptionally > 100-fold uponDicer loss and is resistant to resilencing by complete restoration of miRNA activity. This Dicer-resistant epigenetic switch confers tumorigenicity to these cells. Let-7 targets Imp1–3 are required for this tumorigenicity and feed back to reinforce and sustain expression of the oncogenic network. Together, these Dicer-resistant genes constitute an mRNA expression signature that is present in numerous human cancers and is associated with poor survival.United States. Public Health Service (Grant R01CA133404)National Cancer Institute (U.S.) (Grant P01CA42063)Marie D. and Pierre Casimir-Lamber

A study of central galaxy rotation with stellar mass and environment

© 2017. The American Astronomical Society. All rights reserved. We present a pilot analysis of the influence of galaxy stellar mass and cluster environment on the probability of slow rotation in 22 central galaxies at mean redshift z = 0.07. This includes new integral-field observations of five central galaxies selected from the Sloan Digital Sky Survey, observed with the SPIRAL integral-field spectrograph on the Anglo-Australian Telescope. The composite sample presented here spans a wide range of stellar masses, 10.9 < log(M∗/M⊙)lt; 12.0, and are embedded in halos ranging from groups to clusters, 12.9 < log(M 200 Ṁ) < 15.6. We find a mean probability of slow rotation in our sample of P(SR) = 54 ± 7%. Our results show an increasing probability of slow rotation in central galaxies with increasing stellar mass. However, when we examine the dependence of slow rotation on host cluster halo mass, we do not see a significant relationship. We also explore the influence of cluster dominance on slow rotation in central galaxies. Clusters with low dominance are associated with dynamically younger systems. We find that cluster dominance has no significant effect on the probability of slow rotation in central galaxies. These results conflict with a paradigm in which halo mass alone predetermines central galaxy properties

Dynamic clamp with StdpC software

Dynamic clamp is a powerful method that allows the introduction of artificial electrical components into target cells to simulate ionic conductances and synaptic inputs. This method is based on a fast cycle of measuring the membrane potential of a cell, calculating the current of a desired simulated component using an appropriate model and injecting this current into the cell. Here we present a dynamic clamp protocol using free, fully integrated, open-source software (StdpC, for spike timing-dependent plasticity clamp). Use of this protocol does not require specialist hardware, costly commercial software, experience in real-time operating systems or a strong programming background. The software enables the configuration and operation of a wide range of complex and fully automated dynamic clamp experiments through an intuitive and powerful interface with a minimal initial lead time of a few hours. After initial configuration, experimental results can be generated within minutes of establishing cell recording