Replay across Experiments: A Natural Extension of Off-Policy RL

Replaying data is a principal mechanism underlying the stability and data efficiency of off-policy reinforcement learning (RL). We present an effective yet simple framework to extend the use of replays across multiple experiments, minimally adapting the RL workflow for sizeable improvements in controller performance and research iteration times. At its core, Replay Across Experiments (RaE) involves reusing experience from previous experiments to improve exploration and bootstrap learning while reducing required changes to a minimum in comparison to prior work. We empirically show benefits across a number of RL algorithms and challenging control domains spanning both locomotion and manipulation, including hard exploration tasks from egocentric vision. Through comprehensive ablations, we demonstrate robustness to the quality and amount of data available and various hyperparameter choices. Finally, we discuss how our approach can be applied more broadly across research life cycles and can increase resilience by reloading data across random seeds or hyperparameter variations

Alignment of Free-Space Coupling of Few-Mode Fibre to Multi-Mode Fibre using Digital Holography

Off-axis digital holography is used to align a few-mode fiber to a multi-mode fiber in a free-space optical setup. Alignment based on power coupling measurements alone cannot guarantee low mode-dependent loss. The proposed alignment method enables reliable fiber coupling with low mode-dependent loss and crosstalk

The Mice at play in the CALIFA survey: A case study of a gas-rich major merger between first passage and coalescence

We present optical integral field spectroscopy (IFS) observations of the Mice, a major merger between two massive (>10^11Msol) gas-rich spirals NGC4676A and B, observed between first passage and final coalescence. The spectra provide stellar and gas kinematics, ionised gas properties and stellar population diagnostics, over the full optical extent of both galaxies. The Mice provide a perfect case study highlighting the importance of IFS data for improving our understanding of local galaxies. The impact of first passage on the kinematics of the stars and gas has been significant, with strong bars likely induced in both galaxies. The barred spiral NGC4676B exhibits a strong twist in both its stellar and ionised gas disk. On the other hand, the impact of the merger on the stellar populations has been minimal thus far: star formation induced by the recent close passage has not contributed significantly to the global star formation rate or stellar mass of the galaxies. Both galaxies show bicones of high ionisation gas extending along their minor axes. In NGC4676A the high gas velocity dispersion and Seyfert-like line ratios at large scaleheight indicate a powerful outflow. Fast shocks extend to ~6.6kpc above the disk plane. The measured ram pressure and mass outflow rate (~8-20Msol/yr) are similar to superwinds from local ULIRGs, although NGC4676A has only a moderate infrared luminosity of 3x10^10Lsol. Energy beyond that provided by the mechanical energy of the starburst appears to be required to drive the outflow. We compare the observations to mock kinematic and stellar population maps from a merger simulation. The models show little enhancement in star formation during and following first passage, in agreement with the observations. We highlight areas where IFS data could help further constrain the models.Comment: 23 pages, 13 figures, accepted to A&A. A version with a complete set of high resolution figures is available here: http://www-star.st-and.ac.uk/~vw8/resources/mice_v8_astroph.pd

Pneumocystis jirovecii in General Population

P. jirovecii colonization can be frequently detected in immunocompetent adults, which suggests that the general population could be a source of this infection

Solving Weighted Least Squares (WLS) problems on ARM-based architectures

TheWeighted Least Squares algorithm (WLS) is applied to numerous optimization problems, but requires the use of high computational resources, especially when complex arithmetic is involved. This work aims to accelerate the resolution of a WLS problem by reducing the computational cost (relaying on BLAS/LAPACK routines) and the computational precision from double to single. As a test case, we design an IIR filter for a Graphic Equalizer, where the numerical errors due to single precision are easily visualized. In addition, given the importance of low power architectures for this kind of implementations, we evaluate the performance, scalability, and energy efficiency of each method on two different processors implementing the ARMv7 architecture, widely used in current mobile devices with power constraints. Results show that the method that exhibits a high theoretical computational cost overcomes in efficiency other methods with lower theoretical cost in architectures of this type.This work started in spring 2016 when Jose A. Belloch was a visiting postdoctoral researcher at Budapest University of Technology and Economics thanks to the European Network COST Action IC1305 inside the program Short Term Scientific Mission with the following reference: COST-SPASM-ECOST-STSM-IC1305-020416-072431. Dr. Jose A. Belloch is supported by GVA contract APOSTD/2016/069. The researchers from Universitat Jaume I are supported by the CICYT projects TIN2014-53495-R of MINECO and FEDER. The authors from the Universitat Politecnica de Valencia are supported by MINECO Projects TEC2015-67387-C4-1-R, PROMETEOII/2014/003 and CAPAP-H5 network TIN2014-53522-REDT. The researcher from UCM is supported by the EU (FEDER) and the Spanish MINECO, under Grants TIN 2015-65277-R and TIN2012-32180. The work of Balazs Bank was supported by the UNKP-16-4-III New National Excellence Program of the Ministry of Human Capacities, Hungary.Belloch Rodríguez, JA.; Bank, B.; Igual Peña, FD.; Quintana Ortí, ES.; Vidal Maciá, AM. (2017). Solving Weighted Least Squares (WLS) problems on ARM-based architectures. Journal of Supercomputing. 73(1):530-542. https://doi.org/10.1007/s11227-016-1910-9S530542731Smith TM, van de Geijn RA, Smelyanskiy M, Hammond JR, Van Zee FG (2014) Anatomy of high-performance many-threaded matrix multiplication. In: 28th IEEE International Parallel and Distributed Processing Symposium (IPDPS 2014)Burrus CS (2012) Iterative reweighted least squares. OpenStax-CNC document, May 2012, module m45285. http://cnx.org/content/m45285/1.12 . Accessed 2 Nov 2016Khang SW (1972) Best $$L_p$$ L p approximation. Math Comput 26(118):505–508Jackson LB (2008) Frequency-domain Steiglitz-McBride method for least-squares filter design, ARMA modeling, and periodogram smoothing. IEEE Signal Process Lett 15:49–52Bank B (2012) Magnitude-priority filter design for audio applications. In: Proceedings of $$132^{{\rm nd}}$$ 132 nd AES Convention, Preprint No. 8591, Budapest, Hungary, May 2012Daubechies I, Devire R, Fornasier M, Gntrk CS (2010) Iteratively reweighted least squares minimization for sparse recovery. Comput Music J 23(2):52–69Rämö J, Välimäki V, Bank B (2014) High-precision parallel graphic equalizer. IEEE/ACM Trans Audio Speech Lange Proc 22(12):1894–1904Perez Gonzales E, Reiss J (2009) Automatic equalization of multi-channel audio using cross-adaptive methods. In: Proceedings of AES 127th Convention, New York, Oct. 2009Rämö J, Välimäki V (2013) Live sound equalization and attenuation with a headset. In: Proceedings of AES 51st International Conference, Helsinki, Finland, Aug. 2013Mäkivirta A, Antsalo P, Karjalainen M, Välimäki V (2003) Modal equalization of loudspeaker-room responses at low frequencies. J Audio Eng Soc 51(5):324–343Holters M, Zölzer U (2006) Graphic equalizer design using higher-order recursive filters. In: Proceedings of International Conference Digital Audio Effects, Montreal, QC, pp 37–40Tassart S (2013) Graphical equalization using interpolated filter banks. J Audio Eng Soc 61(5):263–279Chen Z, Geng GS, Yin FL, Hao J (2014) A pre-distortion based design method for digital audio graphic equalizer. Digital Signal Process 25:296–302Välimäki V, Reiss J (2016) All about audio equalization: solutions and frontiers. Appl Sci 6(5):129–145Belloch JA, Välimäki V (2016) Efficient target-response interpolation for a graphic equalizer. In: 2016 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), March 2016, pp 564–568Belloch JA, Alventosa FJ, Alonso P, Quintana-Ortí ES, Vidal AM (2016) Accelerating multi-channel filtering of audio signal on arm processors. J Supercomput, pp 1–12. doi: 10.1007/s11227-016-1689-8Belloch JA, Gonzalez A, Igual FD, Mayo R, Quintana-Ortí ES (2015)Vectorization of binaural sound virtualization on the ARM cortex-A15 architecture. In: Proceedings of 23rd European Signal Processing Conference, (EUSIPCO), Nize, France, September 2015Mitra G, Johnston B, Rendell A, McCreath E, Zhou J (2013) Use of simd vector operations to accelerate application code performance on low-powered arm and intel platforms. In: IEEE 27th International Parallel and Distributed Processing Symposium Workshops PhD Forum (IPDPSW), May 2013, pp 1107–1116Tomov S, Dongarra J, Baboulin M (2008) Towards dense linear algebra for hybrid gpu accelerated manycore systems. LAPACK Working Note, Tech. Rep. 210, Oct. 2008. http://www.netlib.org/lapack/lawnspdf/lawn210.pdf . Accessed 2 Nov 2016Dongarra JJ, DuCroz J, Hammarling S, Hanson RJ (1985) A proposal for an extended set of fortran basic linear algebra subprograms. ACM Signum Newsletter, New York, pp 2–18Golub GH, Loan CFV (2013) Matrix Comput, 4th edn. The John Hopkins University Press, BaltimoreAlonso P, Badia RM, Labarta J, Barreda M, Dolz MF, Mayo R, Quintana-Ortí ES, Reyes R (2012) Tools for power-energy modelling and analysis of parallel scientific applications. In: 41st International Conference on Parallel Processing—ICPP, 2012, pp 420–42

Gammapy: A Python package for gamma-ray astronomy

In this article, we present Gammapy, an open-source Python package for the analysis of astronomical $\gamma$-ray data, and illustrate the functionalities of its first long-term-support release, version 1.0. Built on the modern Python scientific ecosystem, Gammapy provides a uniform platform for reducing and modeling data from different $\gamma$-ray instruments for many analysis scenarios. Gammapy complies with several well-established data conventions in high-energy astrophysics, providing serialized data products that are interoperable with other software packages. Starting from event lists and instrument response functions, Gammapy provides functionalities to reduce these data by binning them in energy and sky coordinates. Several techniques for background estimation are implemented in the package to handle the residual hadronic background affecting $\gamma$-ray instruments. After the data are binned, the flux and morphology of one or more $\gamma$-ray sources can be estimated using Poisson maximum likelihood fitting and assuming a variety of spectral, temporal, and spatial models. Estimation of flux points, likelihood profiles, and light curves is also supported. After describing the structure of the package, we show, using publicly available $\gamma$-ray data, the capabilities of Gammapy in multiple traditional and novel $\gamma$-ray analysis scenarios, such as spectral and spectro-morphological modeling and estimations of a spectral energy distribution and a light curve. Its flexibility and power are displayed in a final multi-instrument example, where datasets from different instruments, at different stages of data reduction, are simultaneously fitted with an astrophysical flux model.Comment: 26 pages, 16 figure

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

Severe Acute Respiratory Syndrome Coronavirus Envelope Protein Regulates Cell Stress Response and Apoptosis

Severe acute respiratory syndrome virus (SARS-CoV) that lacks the envelope (E) gene (rSARS-CoV-ΔE) is attenuated in vivo. To identify factors that contribute to rSARS-CoV-ΔE attenuation, gene expression in cells infected by SARS-CoV with or without E gene was compared. Twenty-five stress response genes were preferentially upregulated during infection in the absence of the E gene. In addition, genes involved in signal transduction, transcription, cell metabolism, immunoregulation, inflammation, apoptosis and cell cycle and differentiation were differentially regulated in cells infected with rSARS-CoV with or without the E gene. Administration of E protein in trans reduced the stress response in cells infected with rSARS-CoV-ΔE or with respiratory syncytial virus, or treated with drugs, such as tunicamycin and thapsigargin that elicit cell stress by different mechanisms. In addition, SARS-CoV E protein down-regulated the signaling pathway inositol-requiring enzyme 1 (IRE-1) of the unfolded protein response, but not the PKR-like ER kinase (PERK) or activating transcription factor 6 (ATF-6) pathways, and reduced cell apoptosis. Overall, the activation of the IRE-1 pathway was not able to restore cell homeostasis, and apoptosis was induced probably as a measure to protect the host by limiting virus production and dissemination. The expression of proinflammatory cytokines was reduced in rSARS-CoV-ΔE-infected cells compared to rSARS-CoV-infected cells, suggesting that the increase in stress responses and the reduction of inflammation in the absence of the E gene contributed to the attenuation of rSARS-CoV-ΔE

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. The consortium generated over 427 million long-read sequences from cDNA and direct RNA datasets, encompassing human, mouse, and manatee species, using different protocols and sequencing platforms. These data were utilized by developers to address challenges in transcript isoform detection and quantification, as well as de novo transcript isoform identification. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. When aiming to detect rare and novel transcripts or when using reference-free approaches, incorporating additional orthogonal data and replicate samples are advised. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis

Epigenetic Signatures Associated with Different Levels of Differentiation Potential in Human Stem Cells

BACKGROUND: The therapeutic use of multipotent stem cells depends on their differentiation potential, which has been shown to be variable for different populations. These differences are likely to be the result of key changes in their epigenetic profiles. METHODOLOGY/PRINCIPAL FINDINGS: to address this issue, we have investigated the levels of epigenetic regulation in well characterized populations of pluripotent embryonic stem cells (ESC) and multipotent adult stem cells (ASC) at the trancriptome, methylome, histone modification and microRNA levels. Differences in gene expression profiles allowed classification of stem cells into three separate populations including ESC, multipotent adult progenitor cells (MAPC) and mesenchymal stromal cells (MSC). The analysis of the PcG repressive marks, histone modifications and gene promoter methylation of differentiation and pluripotency genes demonstrated that stem cell populations with a wider differentiation potential (ESC and MAPC) showed stronger representation of epigenetic repressive marks in differentiation genes and that this epigenetic signature was progressively lost with restriction of stem cell potential. Our analysis of microRNA established specific microRNA signatures suggesting specific microRNAs involved in regulation of pluripotent and differentiation genes. CONCLUSIONS/SIGNIFICANCE: Our study leads us to propose a model where the level of epigenetic regulation, as a combination of DNA methylation and histone modification marks, at differentiation genes defines degrees of differentiation potential from progenitor and multipotent stem cells to pluripotent stem cells