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CiteULike: Everyone's library

CiteULike: Everyone's library


Nonparametric measures of association between a spatial point process and a random set, with geological applications


Journal of the Royal Statistical Society: Series C (Applied Statistics), Vol. 51, No. 2. (1 May 2002), pp. 165-182, doi:10.1111/1467-9876.00261

In mining exploration it is often desired to predict the occurrence of ore deposits given other geological information, such as the locations of faults. More generally it is of interest to measure the spatial association between two spatial patterns observed in the same survey region. Berman developed parametric methods for conditional inference about a point process X given another spatial process Y. This paper proposes an alternative, nonparametric, approach using distance methods, analogous to the use of the summary functions F, G and J for univariate point patterns. Our methods apply to a bivariate spatial process (X, Y) consisting of a point process X and a random set Y. In particular we develop a bivariate analogue of the J-function of van Lieshout and Baddeley which shows promise as a summary statistic and turns out to be closely related to Berman's analysis. Properties of the bivariate J-function include a multiplicative identity under independent superposition, which has no analogue in the univariate case. Two geological examples are investigated.
Rob Foxall, Adrian Baddeley

Genome-wide meta-analysis associates HLA-DQA1/DRB1 and LPA and lifestyle factors with human longevity


Nature Communications, Vol. 8, No. 1. (13 October 2017), doi:10.1038/s41467-017-00934-5
Peter Joshi, Nicola Pirastu, Katherine Kentistou, Krista Fischer, Edith Hofer, Katharina Schraut, David Clark, Teresa Nutile, Catriona Barnes, Paul Timmers, Xia Shen, Ilaria Gandin, Aaron McDaid, Thomas Hansen, Scott Gordon, Franco Giulianini, Thibaud Boutin, Abdel Abdellaoui, Wei Zhao, Carolina Medina-Gomez, Traci Bartz, Stella Trompet, Leslie Lange, Laura Raffield, Ashley van der Spek, Tessel Galesloot, Petroula Proitsi, Lisa Yanek, Lawrence Bielak, Antony Payton, Federico Murgia, Maria Concas, Ginevra Biino, Salman Tajuddin, Ilkka Seppälä, Najaf Amin, Eric Boerwinkle, Anders Børglum, Archie Campbell, Ellen Demerath, Ilja Demuth, Jessica Faul, Ian Ford, Alessandro Gialluisi, Martin Gögele, MariaElisa Graff, Aroon Hingorani, Jouke-Jan Hottenga, David Hougaard, Mikko Hurme, Arfan Ikram, Marja Jylhä, Diana Kuh, Lannie Ligthart, Christina Lill, Ulman Lindenberger, Thomas Lumley, Reedik Mägi, Pedro Marques-Vidal, Sarah Medland, Lili Milani, Reka Nagy, William Ollier, Patricia Peyser, Peter Pramstaller, Paul Ridker, Fernando Rivadeneira, Daniela Ruggiero, Yasaman Saba, Reinhold Schmidt, Helena Schmidt, Eline Slagboom, Blair Smith, Jennifer Smith, Nona Sotoodehnia, Elisabeth Steinhagen-Thiessen, Frank van Rooij, André Verbeek, Sita Vermeulen, Peter Vollenweider, Yunpeng Wang, Thomas Werge, John Whitfield, Alan Zonderman, Terho Lehtimäki, Michele Evans, Mario Pirastu, Christian Fuchsberger, Lars Bertram, Neil Pendleton, Sharon Kardia, Marina Ciullo, Diane Becker, Andrew Wong, Bruce Psaty, Cornelia van Duijn, James Wilson, Wouter Jukema, Lambertus Kiemeney, André Uitterlinden, Nora Franceschini, Kari North, David Weir, Andres Metspalu, Dorret Boomsma, Caroline Hayward, Daniel Chasman, Nicholas Martin, Naveed Sattar, Harry Campbell, Tōnu Esko, Zoltán Kutalik, James Wilson

Virus Population Dynamics and Acquired Virus Resistance in Natural Microbial Communities


Science, Vol. 320, No. 5879. (23 May 2008), pp. 1047-1050, doi:10.1126/science.1157358

Viruses shape microbial community structure and function by altering the fitness of their hosts and by promoting genetic exchange. The complexity of most natural ecosystems has precluded detailed studies of virus-host interactions. We reconstructed virus and host bacterial and archaeal genome sequences from community genomic data from two natural acidophilic biofilms. Viruses were matched to their hosts by analyzing spacer sequences that occur among clustered regularly interspaced short palindromic repeats (CRISPRs) that are a hallmark of virus resistance. Virus population genomic analyses provided evidence that extensive recombination shuffles sequence motifs sufficiently to evade CRISPR spacers. Only the most recently acquired spacers match coexisting viruses, which suggests that community stability is achieved by rapid but compensatory shifts in host resistance levels and virus population structure.
Anders Andersson, Jillian Banfield

Antimalarial Inhibitors Targeting Serine Hydroxymethyltransferase (SHMT) with in Vivo Efficacy and Analysis of their Binding Mode Based on X-ray Cocrystal Structures.


Journal of medicinal chemistry, Vol. 60, No. 12. (22 June 2017), pp. 4840-4860

Target-based approaches toward new antimalarial treatments are highly valuable to prevent resistance development. We report several series of pyrazolopyran-based inhibitors targeting the enzyme serine hydroxymethyltransferase (SHMT), designed to improve microsomal metabolic stability and to identify suitable candidates for in vivo efficacy evaluation. The best ligands inhibited Plasmodium falciparum (Pf) and Arabidopsis thaliana (At) SHMT in target assays and PfNF54 strains in cell-based assays with values in the low nanomolar range (3.2-55 nM). A set of carboxylate derivatives demonstrated markedly improved in vitro metabolic stability (t1/2 > 2 h). A selected ligand showed significant in vivo efficacy with 73% of parasitemia reduction in a mouse model. Five new cocrystal structures with PvSHMT were solved at 2.3-2.6 Å resolution, revealing a unique water-mediated interaction with Tyr63 at the end of the para-aminobenzoate channel. They also displayed the high degree of conformational flexibility of the Cys364-loop lining this channel.
Geoffrey Schwertz, Matthias Witschel, Matthias Rottmann, Roger Bonnert, Ubolsree Leartsakulpanich, Penchit Chitnumsub, Aritsara Jaruwat, Wanwipa Ittarat, Anja Schäfer, Raphael Aponte, Susan Charman, Karen White, Abhijit Kundu, Surajit Sadhukhan, Mel Lloyd, Gail Freiberg, Myron Srikumaran, Marc Siggel, Adrian Zwyssig, Pimchai Chaiyen, François Diederich

Designing novel inhibitors against histone acetyltransferase (HAT: GCN5) of Plasmodium falciparum.


European journal of medicinal chemistry, Vol. 138 (29 September 2017), pp. 26-37

During active proliferation phase of intra-erythrocytic cycle, the genome of P. falciparum is regulated epigenetically and evolutionary conserved parasite-specific histone proteins are extensively acetylated. The reversible process of lysine acetylation, causing transcriptional activation and its deacetylation, causing transcriptional repression is regulated by balanced activities of HATs and HDACs. They are also known to regulate antigenic variations and gametocytic conversion in P. falciparum. These histone modifying enzymes have been identified as potential targets for development of anitmalarials in literature. PfGCN5, a HAT family member of P. falciparum is predominantly involved in H3K9 acetylation. In this study, through comparative structure and sequence analysis, we elucidate differences in the catalytic pocket of PfGCN5 which can be exploited to design selective inhibitors. Through virtual screening of known antimalarials from ChEMBL bioassay database, we mapped 10 compounds with better affinity towards PfGCN5. Further, we identified 10 more novel compounds which showed remarkably better affinity towards the Plasmodium target from analogues of mapped inhibitors from ZINC database of commercially available compounds. Comparative molecular dynamics simulation study of one of the compounds (C14) complex with PfGCN5 and HsGCN5 suggested the possible reason for its selectivity. In vitro parasite growth assay in the presence of C14 showed IC50 value at lower nanomolar range (∼ 225 nM). However, no effect in mammalian fibroblast cells was observed for C14 (up to 20 μM). Further, reduced level of HAT activity of recombinant GCN5 and H3K9Ac was observed in the parasites treated with C14. Overall, this study reports 20 potential inhibitors of PfGCN5 and experimental validation of one molecule (C14) with antimalarial activity at low nanomolar range. Copyright © 2017 Elsevier Masson SAS. All rights reserved.
Amarjeet Kumar, Krishanu Bhowmick, Kunwar Somesh Vikramdeo, Neelima Mondal, Naidu Subbarao, Suman Kumar Dhar

Biological Studies and Target Engagement of the 2-C-Methyl-d-Erythritol 4-Phosphate Cytidylyltransferase (IspD)-Targeting Antimalarial Agent (1R,3S)-MMV008138 and Analogs.


ACS infectious diseases (07 November 2017)

Malaria continues to be one of the deadliest diseases worldwide, and the emergence of drug resistance parasites is a constant threat. Plasmodium parasites utilize the methylerythritol phosphate (MEP) pathway to synthesize isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP), which are essential for parasite growth. Previously, we and others identified that the Malaria Box compound MMV008138 targets the apicoplast and that parasite growth inhibition by this compound can be reversed by supplementation of IPP. Further work has revealed that MMV008138 targets the enzyme 2-C-methyl-d-erythritol 4-phosphate cytidylyltransferase (IspD) in the MEP pathway, which converts MEP and cytidine triphosphate (CTP) to cytidinediphosphate methylerythritol (CDP-ME) and pyrophosphate. In this work, we sought to gain insight into the structure-activity relationships by probing the ability of MMV008138 analogs to inhibit PfIspD recombinant enzyme. Here, we report PfIspD inhibition data for fosmidomycin (FOS) and 19 previously disclosed analogs and report parasite growth and PfIspD inhibition data for 27 new analogs of MMV008138. In addition, we show that MMV008138 does not target the recently characterized human IspD, reinforcing MMV008138 as a prototype of a new class of species-selective IspD-targeting antimalarial agents.
Maryam Ghavami, Emilio Merino, Zhong-Ke Yao, Rubayet Elahi, Morgan Simpson, Maria Fernández-Murga, Joshua Butler, Michael Casasanta, Priscilla Krai, Maxim Totrov, Daniel Slade, Paul Carlier, Maria Belen Cassera

Blindfold learning of an accurate neural metric


(13 Oct 2017)

The brain has no direct access to physical stimuli, but only to the spiking activity evoked in sensory organs. It is unclear how the brain can structure its representation of the world based on differences between those noisy, correlated responses alone. Here we show how to build a distance map of responses from the structure of the population activity of retinal ganglion cells, allowing for the accurate discrimination of distinct visual stimuli from the retinal response. We introduce the Temporal Restricted Boltzmann Machine to learn the spatiotemporal structure of the population activity, and use this model to define a distance between spike trains. We show that this metric outperforms existing neural distances at discriminating pairs of stimuli that are barely distinguishable. The proposed method provides a generic and biologically plausible way to learn to associate similar stimuli based on their spiking responses, without any other knowledge of these stimuli.
Christophe Gardella, Olivier Marre, Thierry Mora

Cognition and Type 1 Diabetes in Children and Adolescents.


Diabetes spectrum : a publication of the American Diabetes Association, Vol. 29, No. 4. (November 2016), pp. 197-202

IN BRIEF In children and adolescents with type 1 diabetes, exposure to glycemic extremes (severe hypoglycemia, chronic hyperglycemia, and diabetic ketoacidosis) overlaps with the time period of most active brain and cognitive development, leading to concerns that these children are at risk for cognitive side effects. This article summarizes the existing literature examining the impact of glycemic extremes on cognitive function and brain structure in youth with type 1 diabetes and points out areas for future research.
Allison Cato, Tamara Hershey

On Clustering Time Series Using Euclidean Distance and Pearson Correlation


(10 Jan 2016)

For time series comparisons, it has often been observed that z-score normalized Euclidean distances far outperform the unnormalized variant. In this paper we show that a z-score normalized, squared Euclidean Distance is, in fact, equal to a distance based on Pearson Correlation. This has profound impact on many distance-based classification or clustering methods. In addition to this theoretically sound result we also show that the often used k-Means algorithm formally needs a mod ification to keep the interpretation as Pearson correlation strictly valid. Experimental results demonstrate that in many cases the standard k-Means algorithm generally produces the same results.
Michael Berthold, Frank Höppner

Cellular Computations Underlying Detection of Gaps in Sounds and Lateralizing Sound Sources.


Trends in neurosciences, Vol. 40, No. 10. (October 2017), pp. 613-624

In mammals, acoustic information arises in the cochlea and is transmitted to the ventral cochlear nuclei (VCN). Three groups of VCN neurons extract different features from the firing of auditory nerve fibers and convey that information along separate pathways through the brainstem. Two of these pathways process temporal information: octopus cells detect coincident firing among auditory nerve fibers and transmit signals along monaural pathways, and bushy cells sharpen the encoding of fine structure and feed binaural pathways. The ability of these cells to signal with temporal precision depends on a low-voltage-activated K(+) conductance (gKL) and a hyperpolarization-activated conductance (gh). This 'tale of two conductances' traces gap detection and sound lateralization to their cellular and biophysical origins. Copyright © 2017 Elsevier Ltd. All rights reserved.
Donata Oertel, Xiao-Jie Cao, James Ison, Paul Allen

Adaptive Systems for the Dynamic Run-time Optimization of Programs.



An abstract is not available.
Gilbert Hansen

An ultra-dense integrated linkage map for hexaploid chrysanthemum enables multi-allelic QTL analysis.


TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, Vol. 130, No. 12. (December 2017), pp. 2527-2541

We constructed the first integrated genetic linkage map in a polysomic hexaploid. This enabled us to estimate inheritance of parental haplotypes in the offspring and detect multi-allelic QTL. Construction and use of linkage maps are challenging in hexaploids with polysomic inheritance. Full map integration requires calculations of recombination frequency between markers with complex segregation types. In addition, detection of QTL in hexaploids requires information on all six alleles at one locus for each individual. We describe a method that we used to construct a fully integrated linkage map for chrysanthemum (Chrysanthemum × morifolium, 2n = 6x = 54). A bi-parental F1 population of 406 individuals was genotyped with an 183,000 SNP genotyping array. The resulting linkage map consisted of 30,312 segregating SNP markers of all possible marker dosage types, representing nine chromosomal linkage groups and 107 out of 108 expected homologues. Synteny with lettuce (Lactuca sativa) showed local colinearity. Overall, it was high enough to number the chrysanthemum chromosomal linkage groups according to those in lettuce. We used the integrated and phased linkage map to reconstruct inheritance of parental haplotypes in the F1 population. Estimated probabilities for the parental haplotypes were used for multi-allelic QTL analyses on four traits with different underlying genetic architectures. This resulted in the identification of major QTL that were affected by multiple alleles having a differential effect on the phenotype. The presented linkage map sets a standard for future genetic mapping analyses in chrysanthemum and closely related species. Moreover, the described methods are a major step forward for linkage mapping and QTL analysis in hexaploids.
Geert van Geest, Peter Bourke, Roeland Voorrips, Agnieszka Marasek-Ciolakowska, Yanlin Liao, Aike Post, Uulke van Meeteren, Richard Visser, Chris Maliepaard, Paul Arens

Present Without Past: The Disruption of Temporal Integration in a Case of Transsexuality


Psychoanalytic Inquiry, Vol. 36, No. 5. (3 July 2016), pp. 360-370, doi:10.1080/07351690.2016.1180908

ABSTRACTIn this article, I examine the impact of extensive modification of the body on the temporal link, which is an important feature of human identity, as it provides continuity between different representations of the self over time. I illustrate this with a case of a young boy who underwent sex reassignment surgery in late adolescence after the artificial suspension of puberty through sex hormones. I argue that when hormones are used in this way, one can observe in some cases not only the desired suspension of physical time during which the body?s given biological trajectory is artificially halted, but also of psychological time. In some instances, this biological and psychic detour can result in a marked distortion in the young person?s relationship to time and impacts on their psychological adaptation following surgery.
Alessandra Lemma

Algorithms for hierarchical clustering: an overview, II


Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery, Vol. 7, No. 6. (1 November 2017), pp. e1219-n/a, doi:10.1002/widm.1219

We survey agglomerative hierarchical clustering algorithms and discuss efficient implementations that are available in R and other software environments. We look at hierarchical self-organizing maps and mixture models. We review grid-based clustering, focusing on hierarchical density-based approaches. Finally, we describe a recently developed very efficient (linear time) hierarchical clustering algorithm, which can also be viewed as a hierarchical grid-based algorithm. This review adds to the earlier version, Murtagh F, Contreras P. Algorithms for hierarchical clustering: an overview, Wiley Interdiscip Rev: Data Mining Knowl Discov 2012, 2, 86–97. WIREs Data Mining Knowl Discov 2017, 7:e1219. doi: 10.1002/widm.1219 For further resources related to this article, please visit the WIREs website.
Fionn Murtagh, Pedro Contreras

Ward’s Hierarchical Agglomerative Clustering Method: Which Algorithms Implement Ward’s Criterion?


In Journal of Classification, Vol. 31, No. 3. (2014), pp. 274-295, doi:10.1007/s00357-014-9161-z

The Ward error sum of squares hierarchical clustering method has been very widely used since its first description by Ward in a 1963 publication. It has also been generalized in various ways. Two algorithms are found in the literature and software, both announcing that they implement the Ward clustering method. When applied to the same distance matrix, they produce different results. One algorithm preserves Ward’s criterion, the other does not. Our survey work and case studies will be useful for all those involved in developing software for data analysis using Ward’s hierarchical clustering method.
Fionn Murtagh, Pierre Legendre

Fragment Binding to β-Secretase 1 without Catalytic Aspartate Interactions Identified via Orthogonal Screening Approaches.


ACS omega, Vol. 2, No. 2. (28 February 2017), pp. 685-697

An approach to identify β-secretase 1 (BACE1) fragment binders that do not interact with the catalytic aspartate dyad is presented. A ThermoFluor (thermal shift) and a fluorescence resonance energy transfer enzymatic screen on the soluble domain of BACE1, together with a surface plasmon resonance (SPR) screen on the soluble domain of BACE1 and a mutant of one catalytic Asp (D32N), were run in parallel. Fragments that were active in at least two of these assays were further confirmed using one-dimensional NMR (WaterLOGSY) and SPR binding competition studies with peptidic inhibitor OM99-2. Protein-observed NMR (two-dimensional (15)N heteronuclear single-quantum coherence spectroscopy) and crystallographic studies with the soluble domain of BACE1 identified a unique and novel binding mode for compound 12, a fragment that still occupies the active site while not making any interactions with catalytic Asps. This novel approach of combining orthogonal fragment screening techniques, for both wild-type and mutant enzymes, as well as binding competition studies could be generalized to other targets to overcome undesired interaction motifs and as a hit-generation approach in highly constrained intellectual property space.
Frederik Rombouts, Richard Alexander, Erna Cleiren, Alex De Groot, Michel Carpentier, Joyce Dijkmans, Katleen Fierens, Stefan Masure, Diederik Moechars, Martina Palomino-Schätzlein, Antonio Pineda-Lucena, Andrés Trabanco, Daan Van Glabbeek, Ann Vos, Gary Tresadern

Discovery of a Diaminopyrimidine FLT3 Inhibitor Active against Acute Myeloid Leukemia.


ACS omega, Vol. 2, No. 5. (31 May 2017), pp. 1985-2009

Profiling of the kinase-binding capabilities of an aminopyrimidine analogue detected in a cellular screen of the St. Jude small-molecule collection led to the identification of a novel series of FMS-like tyrosine kinase 3 (FLT3) inhibitors. Structure-activity relationship studies led to the development of compounds exhibiting good potency against MV4-11 and MOLM13 acute myelogenous leukemia cells driven by FLT3, regardless of their FLT3 mutation status. In vitro pharmacological profiling demonstrated that compound 5e shows characteristics suitable for further preclinical development.
Jamie Jarusiewicz, Jae Yoon Jeon, Michele Connelly, Yizhe Chen, Lei Yang, Sharyn Baker, Kiplin Guy

Tyrosine kinase inhibition increases the cell surface localization of FLT3-ITD and enhances FLT3-directed immunotherapy of acute myeloid leukemia.


Leukemia (14 August 2017)

The fms-related tyrosine kinase 3 (FLT3) receptor has been extensively studied over the past two decades with regard to oncogenic alterations that do not only serve as prognostic markers but also as therapeutic targets in acute myeloid leukemia (AML). Internal tandem duplications (ITDs) became of special interest in this setting as they are associated with unfavorable prognosis. Because of sequence-dependent protein conformational changes FLT3-ITD tends to autophosphorylate and displays a constitutive intracellular localization. Here, we analyzed the effect of tyrosine kinase inhibitors (TKIs) on the localization of the FLT3 receptor and its mutants. TKI treatment increased the surface expression through upregulation of FLT3 and glycosylation of FLT3-ITD and FLT3-D835Y mutants. In T cell-mediated cytotoxicity (TCMC) assays, using a bispecific FLT3 × CD3 antibody construct, the combination with TKI treatment increased TCMC in the FLT3-ITD-positive AML cell lines MOLM-13 and MV4-11, patient-derived xenograft cells and primary patient samples. Our findings provide the basis for rational combination of TKI and FLT3-directed immunotherapy with potential benefit for FLT3-ITD-positive AML patients.Leukemia advance online publication, 12 September 2017; doi:10.1038/leu.2017.257.
K Reiter, H Polzer, C Krupka, A Maiser, B Vick, M Rothenberg-Thurley, KH Metzeler, D Dörfel, HR Salih, G Jung, E Nößner, I Jeremias, W Hiddemann, H Leonhardt, K Spiekermann, M Subklewe, PA Greif

Gaming out online: Black lesbian identity development and community building in Xbox Live


Journal of Lesbian Studies (22 November 2017), pp. 1-15, doi:10.1080/10894160.2018.1384293

ABSTRACTAs gaming culture continues to marginalize women and people of color, other gamers are also highlighting the inequalities they face within digital gaming communities. While heterosexism and homophobia are commonplace within gaming culture, little is known about the actual experiences of ?gaymers? and even less about ?gaymers? of color. As such, this article seeks to explore lesbians of color and their experiences ?gayming? out and online. Exploring identity development, community building, and connectivity via social networking, the women within this study articulate what it means to be lesbian online and how this impacts their physical and digital experiences. The private spaces within gaming culture that many marginalized groups inhabit are the few spaces that value the articulation of marginalized interests and viewpoints. Ethnographic observations reveal how supportive communities can improve resilience by mitigating the effects of stereotyping, microaggressions, and other discriminatory practices in online gaming.
Kishonna Gray

Activity theory as a framework for analyzing and redesigning work


Ergonomics, Vol. 43, No. 7. (1 July 2000), pp. 960-974, doi:10.1080/001401300409143

Cultural-historical activity theory is a new framework aimed at transcending the dichotomies of micro- and macro-, mental and material, observation and intervention in analysis and redesign of work. The approach distinguishes between short-lived goal-directed actions and durable, object-oriented activity systems. A historically evolving collective activity system, seen in its network relations to other activity systems, is taken as the prime unit of analysis against which scripted strings of goal-directed actions and automatic operations are interpreted. Activity systems are driven by communal motives that are often difficult to articulate for individual participants. Activity systems are in constant movement and internally contradictory. Their systemic contradictions, manifested in disturbances and mundane innovations, offer possibilities for expansive developmental transformations. Such transformations proceed through stepwise cycles of expansive learning which begin with actions of questioning the existing standard practice, then proceed to actions of analyzing its contradictions and modelling a vision for its zone of proximal development, then to actions of examining and implementing the new model in practice. New forms of work organization increasingly require negotiated ?knotworking? across boundaries. Correspondingly, expansive learning increasingly involves horizontal widening of collective expertise by means of debating, negotiating and hybridizing different perspectives and conceptualizations. Findings from a longitudinal intervention study of children's medical care illuminate the theoretical arguments.
Yrjo Engestrom

Mastering the game of Go with deep neural networks and tree search


Nature, Vol. 529, No. 7587. (27 January 2016), pp. 484-489, doi:10.1038/nature16961

The game of Go has long been viewed as the most challenging of classic games for artificial intelligence owing to its enormous search space and the difficulty of evaluating board positions and moves. Here we introduce a new approach to computer Go that uses ‘value networks’ to evaluate board positions and ‘policy networks’ to select moves. These deep neural networks are trained by a novel combination of supervised learning from human expert games, and reinforcement learning from games of self-play. Without any lookahead search, the neural networks play Go at the level of state-of-the-art Monte Carlo tree search programs that simulate thousands of random games of self-play. We also introduce a new search algorithm that combines Monte Carlo simulation with value and policy networks. Using this search algorithm, our program AlphaGo achieved a 99.8% winning rate against other Go programs, and defeated the human European Go champion by 5 games to 0. This is the first time that a computer program has defeated a human professional player in the full-sized game of Go, a feat previously thought to be at least a decade away.
David Silver, Aja Huang, Chris Maddison, Arthur Guez, Laurent Sifre, George van den Driessche, Julian Schrittwieser, Ioannis Antonoglou, Veda Panneershelvam, Marc Lanctot, Sander Dieleman, Dominik Grewe, John Nham, Nal Kalchbrenner, Ilya Sutskever, Timothy Lillicrap, Madeleine Leach, Koray Kavukcuoglu, Thore Graepel, Demis Hassabis

Inception-v4, Inception-ResNet and the Impact of Residual Connections on Learning


(23 Aug 2016)

Very deep convolutional networks have been central to the largest advances in image recognition performance in recent years. One example is the Inception architecture that has been shown to achieve very good performance at relatively low computational cost. Recently, the introduction of residual connections in conjunction with a more traditional architecture has yielded state-of-the-art performance in the 2015 ILSVRC challenge; its performance was similar to the latest generation Inception-v3 network. This raises the question of whether there are any benefit in combining the Inception architecture with residual connections. Here we give clear empirical evidence that training with residual connections accelerates the training of Inception networks significantly. There is also some evidence of residual Inception networks outperforming similarly expensive Inception networks without residual connections by a thin margin. We also present several new streamlined architectures for both residual and non-residual Inception networks. These variations improve the single-frame recognition performance on the ILSVRC 2012 classification task significantly. We further demonstrate how proper activation scaling stabilizes the training of very wide residual Inception networks. With an ensemble of three residual and one Inception-v4, we achieve 3.08 percent top-5 error on the test set of the ImageNet classification (CLS) challenge
Christian Szegedy, Sergey Ioffe, Vincent Vanhoucke, Alex Alemi

Symmetry control of nanorod superlattice driven by a governing force


Nature Communications, Vol. 8, No. 1. (10 November 2017), doi:10.1038/s41467-017-01111-4
Yujia Liang, Yong Xie, Dongxue Chen, Chuanfei Guo, Shuai Hou, Tao Wen, Fengyou Yang, Ke Deng, Xiaochun Wu, Ivan Smalyukh, Qian Liu

Thermal dynamics of pulsed-laser excited gold nanorods in suspension


Nanoscale, Vol. 9, No. 44. (2017), pp. 17284-17292, doi:10.1039/c7nr06125k

Photothermal reactions of metallic nanostructures, such as gold nanorods show appealing structural relaxations, such as bubble formation or particle modification. We have employed a pump-probe method to record the structural relaxations of a suspension of gold nanorods upon femtosecond laser excitation by pulsed X-ray scattering both with wide-angle and small-angle sensitivity. Single-pulse reactions include transient bubble formation at 20 J m-2 and irreversible nanorod reshaping at 30 J m-2. Thus the window for reversible excitation is very narrow. Additionally we could map the time-domain and fluence behaviour in a wide range to characterize the relaxations comprehensively. The polarized laser pulse first selectively excites nanorods aligned with the laser electric field, but at higher fluence non-aligned rods are also transformed. At low fluence this transformation happens in the solid state, while at higher fluence the rods melt.
Anton Plech, Shyjumon Ibrahimkutty, Stefan Reich, Gemma Newby

Advanced electron tomography of nanoparticle assemblies


EPL (Europhysics Letters), Vol. 119, No. 3. (01 August 2017), 38001, doi:10.1209/0295-5075/119/38001
T Altantzis, D Zanaga, S Bals

Sensitivity of Turbine-Height Wind Speeds to Parameters in Planetary Boundary-Layer and Surface-Layer Schemes in the Weather Research and Forecasting Model


In Boundary-Layer Meteorology, Vol. 162, No. 1. (2017), pp. 117-142, doi:10.1007/s10546-016-0185-2

We evaluate the sensitivity of simulated turbine-height wind speeds to 26 parameters within the Mellor–Yamada–Nakanishi–Niino (MYNN) planetary boundary-layer scheme and MM5 surface-layer scheme of the Weather Research and Forecasting model over an area of complex terrain. An efficient sampling algorithm and generalized linear model are used to explore the multiple-dimensional parameter space and quantify the parametric sensitivity of simulated turbine-height wind speeds. The results indicate that most of the variability in the ensemble simulations is due to parameters related to the dissipation of turbulent kinetic energy (TKE), Prandtl number, turbulent length scales, surface roughness, and the von Kármán constant. The parameter associated with the TKE dissipation rate is found to be most important, and a larger dissipation rate produces larger hub-height wind speeds. A larger Prandtl number results in smaller nighttime wind speeds. Increasing surface roughness reduces the frequencies of both extremely weak and strong airflows, implying a reduction in the variability of wind speed. All of the above parameters significantly affect the vertical profiles of wind speed and the magnitude of wind shear. The relative contributions of individual parameters are found to be dependent on both the terrain slope and atmospheric stability.
Ben Yang, Yun Qian, LarryK Berg, Po-Lun Ma, Sonia Wharton, Vera Bulaevskaya, Huiping Yan, Zhangshuan Hou, WilliamJ Shaw

Enhanced Thermal Stability and Biocompatibility of Gold Nanorods by Graphene Oxide


In Plasmonics (2017), pp. 1-10, doi:10.1007/s11468-017-0667-1
Vahid Shirshahi, Shadie Hatamie, SeyedNasrollah Tabatabaei, Marzieh Salimi, Reza Saber

Magnetic Resonance Imaging of Pituitary Tumors


Vol. 45 (21 March 2016), pp. 97-120, doi:10.1159/000442327
Jean-François Bonneville

Breast and thyroid cancer and malignant melanoma promoted by alcohol-induced pituitary secretion of prolactin, T.S.H. and M.S.H.


Lancet (London, England), Vol. 1, No. 7967. (08 May 1976), pp. 996-999

In interview data from the U.S.A.'s Third National Cancer Survey, alcohol ingestion was associated with a higher occurrence of cancers of the breast, thyroid, and amlignant melanoma. Data from other studies support the first two associations. A unifying hypothesis to explain these seemingly diverse associations suggests that alcohol stimulates anterior pituitary secretion of prolactin, thyroid-stimulating hormone (T.S.H.), and melanocyte-stimulating hormone (M.S.H.). Under the stimulations of these hormones, the three target tissues exhibit increased mitotic activity and hence an increase susceptibility to the development of a malignancy. A wide variety of findings from other studies indicate plausibility for this hypothesis. The implications could be grave. In addition to alcohol, several common drugs acting in similar manner could be cancer promoters, including: resperine, methyldopa, phenothiaznes, d-amphetamine, tricyclic antidepressants, and antihistamines. Over 20000 (25%) ofall new breast-cancer cases each year in the U.S.A. could be preventable if this hypothesis is correct.
RR Williams

Entanglement manipulation and distillability beyond LOCC


(10 Nov 2017)

When a quantum system is distributed to spatially separated parties, it is natural to consider how the system evolves when the parties perform local quantum operations with classical communication (LOCC). However, the structure of LOCC operations is exceedingly complex leaving many important physical problems unsolved. In this paper we consider generalized resource theories of entanglement based on different relaxations to the class of LOCC. The behavior of various entanglement measures are studied under non-entangling operations, as well as the newly introduced dually non-entangling and PPT-preserving operational classes. In an effort to better understand the nature of LOCC bound entanglement, we study the problem of entanglement distillation in these generalized resource theories. We show that all NPT entangled states can be distilled using operations that are both PPT and dually non-entangling. Furthermore, for any entangled state $ρ$ and any $ε>0$, we prove the existence of a non-entangling map that is $ε$ close to the set of LOCC and which is able to distill pure-state entanglement from $ρ$. This finding reveals a type of fragility to the phenomenon of bound entanglement in LOCC processing. We then turn to the stochastic convertibility of multipartite pure states and show that any two states can be interconverted by any polytope approximation to the set of separable operations. Finally, as an analog to $k$-positive maps, we introduce and analyze the set of $k$-non-entangling operations.
Eric Chitambar, Julio de Vicente, Mark Girard, Gilad Gour

Lie algebra representations and rigged Hilbert spaces: the SO(2) case


(10 Nov 2017)

It is well known that related with the irreducible representations of the Lie group $SO(2)$ we find a discrete basis as well a continuous one. In this paper we revisited this situation under the light of Rigged Hilbert spaces, which are the suitable framework to deal with both discrete and bases in the same context and in relation with physical applications.
Enrico Celeghini, Manuel Gadella, Mariano del Olmo

Experimental study of quantum thermodynamics using optical vortices


(10 Nov 2017)

Non-equilibrium thermodynamics and quantum information theory are interrelated research fields witnessing an increasing interest, both theoretical and experimental. This is manly due to the broadness of these theories, which found applications in many different fields of science, ranging from biology to the foundations of physics. Here, by employing the orbital angular momentum of light, we propose a new platform for studying non-equilibrium properties of high dimensional quantum systems. Specifically, we use Laguerre-Gaussian beams to emulate the energy eigenstates of a two-dimension quantum harmonic oscillator having angular momentum. These light beams are subjected to a process realized by a spatial light modulator and the corresponding work distribution is experimentally reconstructed employing a two-point measurement scheme. The Jarzynski fluctuation relation is then verified. We also demonstrate the operation of the system as a Maxwell's demon.
Medeiros de Araújo, T Häffner, R Bernardi, DS Tasca, MPJ Lavery, MJ Padgett, A Kanaan, LC Céleri, Souto Ribeiro

What $g^(2)(0)<1/2$ tells you - and what it does not


(16 Nov 2017)

Quantum-optical research on semiconductor quantum dots puts special emphasis on the measurement of the second-order correlation function $g^(2)(τ)$, arguing that $g^(2)(0)<1/2$ implies the source field represents a good single-photon light source. We analyze this claim theoretically. A quantum state of light having no projection on the single-photon Fock state can not give a value of $g^(2)(0)<1/2$. However, with solely the value of $g^(2)(0)$, the amplitude of this single-photon projection can be arbitrarily small, owing to vacuum contributions. Yet, one can determine a lower bound on the ratio of single-to-multi-photon emission from $g^(2)(0)$. For a fixed ratio of single-to-multi-photon emission, $g^(2)(0)$ is artificially enhanced by the vacuum contributions. We derive an effective second-order correlation function, which corrects this enhancement, substantially improving the lower bound. The results are applied to theoretical and realized experimental setups and indicate that the quality of solid-state single-photon sources, at least with respect to this criterion, is often underestimated.
Peter Grünwald

Quantum Origami: Applying Transversal Gates and Measuring Topological Order


(15 Nov 2017)

In topology, a torus remains invariant under certain non-trivial transformations known as modular transformations. In the context of topologically ordered quantum states of matter, these transformations encode the braiding statistics and fusion rules of emergent anyonic excitations and thus serve as a diagnostic of topological order. Moreover, modular transformations of higher genus surfaces, e.g. a torus with multiple handles, can enhance the computational power of a topological state, in many cases providing a universal fault-tolerant set of gates for quantum computation. However, due to the intrusive nature of modular transformations, which abstractly involve global operations and manifold surgery, physical implementations of them in local systems have remained elusive. Here, we show that by folding manifolds, modular transformations can be reduced to independent local unitaries, providing a novel class of transversal logic gates in topological states. Specifically, through folding, we demonstrate that multi-layer topological states with appropriate boundary conditions and twist defects allow modular transformations to be effectively implemented by a finite sequence of local SWAP gates between the layers. We further provide methods to directly measure the modular matrices, and thus the fractional statistics of anyonic excitations, providing a novel way to directly measure topological order.
Guanyu Zhu, Mohammad Hafezi, Maissam Barkeshli

Automated detection and cataloging of global explosive volcanism using the International Monitoring System infrasound network


J. Geophys. Res. Solid Earth, Vol. 122, No. 4. (1 April 2017), 2016JB013356, doi:10.1002/2016jb013356

We experiment with a new method to search systematically through multiyear data from the International Monitoring System (IMS) infrasound network to identify explosive volcanic eruption signals originating anywhere on Earth. Detecting, quantifying, and cataloging the global occurrence of explosive volcanism helps toward several goals in Earth sciences and has direct applications in volcanic hazard mitigation. We combine infrasound signal association across multiple stations with source location using a brute-force, grid-search, cross-bearings approach. The algorithm corrects for a background prior rate of coherent unwanted infrasound signals (clutter) in a global grid, without needing to screen array processing detection lists from individual stations prior to association. We develop the algorithm using case studies of explosive eruptions: 2008 Kasatochi, Alaska; 2009 Sarychev Peak, Kurile Islands; and 2010 Eyjafjallajökull, Iceland. We apply the method to global IMS infrasound data from 2005–2010 to construct a preliminary acoustic catalog that emphasizes sustained explosive volcanic activity (long-duration signals or sequences of impulsive transients lasting hours to days). This work represents a step toward the goal of integrating IMS infrasound data products into global volcanic eruption early warning and notification systems. Additionally, a better understanding of volcanic signal detection and location with the IMS helps improve operational event detection, discrimination, and association capabilities.
Robin Matoza, David Green, Alexis Le Pichon, Peter Shearer, David Fee, Pierrick Mialle, Lars Ceranna

Thomas Precession for Dressed Particles


(15 Nov 2017)

We consider a particle dressed with boundary gravitons in three-dimensional Minkowski space. The existence of BMS transformations implies that the particle's wavefunction picks up a Berry phase when subjected to changes of reference frames that trace a closed path in the asymptotic symmetry group. We evaluate this phase and show that, for BMS superrotations, it provides a gravitational generalization of Thomas precession. In principle, such phases are observable signatures of asymptotic symmetries.
Blagoje Oblak

High-harmonic generation in solids with and without topological edge states


(19 Nov 2017)

High-harmonic generation (HHG) in the two topological phases of a finite, one-dimensional, periodic structure is investigated using a self-consistent time-dependent density functional theory (TDDFT) approach. For harmonic photon energies smaller than the band gap, the harmonic yield is found to differ up to fourteen orders of magnitude for the two topological phases. This giant topological effect is explained by the degree of destructive interference in the harmonic emission of all valence-band electrons, which strongly depends on whether topological edge states are present or not.
Dieter Bauer, Kenneth Hansen

The time-reverse of any causal theory is eternal noise


(15 Nov 2017)

We consider a very general class of theories, process theories, which capture the underlying structure common to most theories of physics as we understand them today (be they established, toy or speculative theories). Amongst these theories, we will be focusing on those which are `causal', in the sense that they are intrinsically compatible with the causal structure of space-time -- as required by relativity. We demonstrate that there is a sharp contrast between these theories and the corresponding time-reversed theories, where time is taken to flow backwards from the future to the past. While the former typically feature a rich gamut of allowed states, the latter only allow for a single state: eternal noise. We illustrate this result by considering of the time-reverse of quantum theory. We also derive a strengthening of the result in PRL 108, 200403 on signalling in time-reversed theories.
Bob Coecke, Stefano Gogioso, John Selby

Exploring Energy-Time Entanglement Using Geometric Phase


Physical Review Letters, Vol. 101, No. 18. (14 Nov 2017), doi:10.1103/physrevlett.101.180405

Using the signal and idler photons produced by parametric downconversion, we report an experimental observation of a violation of the Bell inequality for energy and time based purely on the geometric phases of the signal and idler photons. We thus show that energy-time entanglement between the signal and idler photons can be explored by means of their geometric phases. These results may have important practical implications for quantum information science by providing an additional means by which entanglement can be manipulated.
Anand Jha, Mehul Malik, Robert Boyd

Uniqueness of the joint measurement and the structure of the set of compatible quantum measurements


(17 Nov 2017)

We address the problem of characterising the compatible tuples of measurements that admit a unique joint measurement. We derive a uniqueness criterion based on the method of perturbations and apply it to show that extremal points of the set of compatible tuples admit a unique joint measurement, while all tuples that admit a unique joint measurement lie in the boundary of such a set. We also provide counter-examples showing that none of these properties are both necessary and sufficient, thus completely describing the relation between joint measurement uniqueness and the structure of the compatible set. As a by-product of our investigations, we completely characterise the extremal and boundary points of the set of general tuples of measurements and of the subset of compatible tuples.
Leonardo Guerini, Marcelo Cunha

Entanglement, non-Markovianity, and causal non-separability


(11 Nov 2017)

Quantum mechanics, in principle, allows for processes with indefinite causal order. However, most of these causal anomalies have not yet been detected experimentally. We show that every such process can be simulated experimentally by means of non-Markovian dynamics with a measurement on additional degrees of freedom. Explicitly, we provide a constructive scheme to implement arbitrary acausal processes. Furthermore, we give necessary and sufficient conditions for open system dynamics with measurement to yield processes that respect causality locally, and find that tripartite entanglement and nonlocal unitary transformations are crucial requirements for the simulation of causally indefinite processes. These results show a direct connection between three counter-intuitive concepts: non-Markovianity, entanglement, and causal indefiniteness.
Simon Milz, Felix Pollock, Thao Le, Giulio Chiribella, Kavan Modi

Coherent states in a magnetic field and their generalizations


(10 Nov 2017)

This is a brief review of various families of coherent and squeezed states (and their generalizations) for a charged particle in a magnetic field, that have been constructed for the past 50 years. Although the main attention is paid to the Gaussian states, various families of non-Gaussian states are also discussed, and the list of relevant references is provided.
VV Dodonov

Reversing the thermodynamic arrow of time using quantum correlations


(9 Nov 2017)

The second law permits the prediction of the direction of natural processes, thus defining a thermodynamic arrow of time. However, standard thermodynamics presupposes the absence of initial correlations between interacting systems. We here experimentally demonstrate the reversal of the arrow of time for two initially quantum correlated spins-1/2, prepared in local thermal states at different temperatures, employing a Nuclear Magnetic Resonance setup. We observe a spontaneous heat flow from the cold to the hot system. This process is enabled by a trade off between correlations and entropy that we quantify with information-theoretical quantities.
Kaonan Micadei, John Peterson, Alexandre Souza, Roberto Sarthour, Ivan Oliveira, Gabriel Landi, Tiago Batalhão, Roberto Serra, Eric Lutz

Superdensity Operators for Spacetime Quantum Mechanics


(8 Nov 2017)

We introduce superdensity operators as a tool for analyzing quantum information in spacetime. Superdensity operators encode spacetime correlation functions in an operator framework, and support a natural generalization of Hilbert space techniques and Dirac's transformation theory as traditionally applied to standard density operators. Superdensity operators can be measured experimentally, but accessing their full content requires novel procedures. We demonstrate these statements on several examples. The superdensity formalism suggests useful definitions of spacetime entropies and spacetime quantum channels. For example, we show that the von Neumann entropy of a superdensity operator is related to a quantum generalization of the Kolmogorov-Sinai entropy, and compute this for a many-body system. We also suggest experimental protocols for measuring spacetime entropies.
Jordan Cotler, Chao-Ming Jian, Xiao-Liang Qi, Frank Wilczek

Local unitary classification for sets of generalized Bell states


(16 Nov 2017)

In this paper, we study the local unitary classification for sets including two (three) generalized Bell states, called doublet (triplet), based on the local unitary equivalence of two sets. In detail, we firstly introduce some more general unitary operators besides Clifford operators to find out local unitary equivalent sets as many as possible; and then we present two necessary conditions for two local unitary equivalent sets to prove the local inequivalence. According to this thought, we completely classify all the doublets in $d⊗ d$ quantum system into the locally inequivalent doublets exactly with the number of $d$'s factors. Moreover, all the triplets in $p^α⊗ p^α$ quantum system for prime can be partitioned into $\frac(α + 3)6p^α + O(α p^α-1)$ LU-inequivalent triplets, especially, when $α=2$ and $p>2$, there are exactly $\lfloor \frac56p^2\rfloor + \lfloor \fracp-26+(-1)^\lfloor\fracp3\rfloor\fracp3\rfloor + 3$ LU-inequivalent triplets.
Bujiao Wu, Jiaqing Jiang, Jialin Zhang, Guojing Tian, Xiaoming Sun

Geometry of quantum correlations in space-time


(16 Nov 2017)

The traditional formalism of non-relativistic quantum theory allows the state of a quantum system to extend across space, but only restricts it to a single instant in time, leading to distinction between theoretical treatments of spatial and temporal quantum correlations. Here we unify the geometrical description of two-point quantum correlations in space-time. Our study presents the geometry of correlations between two sequential Pauli measurements on a single qubit undergoing an arbitrary quantum channel evolution together with two-qubit spatial correlations under a common framework. We establish a symmetric structure between quantum correlations in space and time. This symmetry is broken in the presence of non-unital channels, which further reveals a set of temporal correlations that are indistinguishable from correlations found in bipartite entangled states.
Zhikuan Zhao, Robert Pisarczyk, Jayne Thompson, Mile Gu, Vlatko Vedral, Joseph Fitzsimons

Is serotonin an upper or a downer? The evolution of the serotonergic system and its role in depression and the antidepressant response


Neuroscience & Biobehavioral Reviews, Vol. 51 (April 2015), pp. 164-188, doi:10.1016/j.neubiorev.2015.01.018
Paul Andrews, Aadil Bharwani, Kyuwon Lee, Molly Fox, Anderson Thomson

The Hahn Quantum System


(16 Nov 2017)

Using a formulation of quantum mechanics based on the theory of orthogonal polynomials, we introduce a four-parameter system associated with the Hahn and continuous Hahn polynomials. The continuum energy scattering states are written in terms of the continuous Hahn polynomial whose asymptotics give the scattering amplitude and phase shift. On the other hand, the finite number of discrete bound states are associated with the Hahn polynomial.
AD Alhaidari, YT Li

Accuracy of magnetic resonance imaging in prediction of tumour-free resection margin in rectal cancer surgery


The Lancet, Vol. 357, No. 9255. (February 2001), pp. 497-504, doi:10.1016/s0140-6736(00)04040-x
RGH Beets-Tan, GL Beets, RFA Vliegen, AGH Kessels, Van Boven, De Bruine, MF von Meyenfeldt, CGMI Baeten, JMA van Engelshoven

The role of magnetic susceptibility in magnetic resonance imaging: MRI magnetic compatibility of the first and second kinds


Med. Phys., Vol. 23, No. 6. (1 June 1996), pp. 815-850, doi:10.1118/1.597854

The concept of magnetic susceptibility is central to many current research and development activities in magnetic resonance imaging (MRI); for example, the development of MR-guided surgery has created a need for surgical instruments and other devices with susceptibility tailored to the MR environment; susceptibility effects can lead to position errors of up to several millimeters in MR-guided stereotactic surgery; and the variation of magnetic susceptibility on a microscopic scale within tissues contributes to MR contrast and is the basis of functional MRI. The magnetic aspects of MR compatibility are discussed in terms of two levels of acceptability: Materials with the first kind of magnetic field compatibility are such that magnetic forces and torques do not interfere significantly when the materials are used within the magnetic field of the scanner; materials with the second kind of magnetic field compatibility meet the more demanding requirement that they produce only negligible artifacts within the MR image and their effect on the positional accuracy of features within the image is negligible or can readily be corrected. Several materials exhibiting magnetic field compatibility of the second kind have been studied and a group of materials that produce essentially no image distortion, even when located directly within the imaging field of view, is identified. Because of demagnetizing effects, the shape and orientation, as well as the susceptibility, of objects within and adjacent to the imaging region is important in MRI. The quantitative use of susceptibility data is important to MRI, but the use of literature values for the susceptibility of materials is often difficult because of inconsistent traditions in the definitions and units used for magnetic parameters—particularly susceptibility. The uniform use of SI units for magnetic susceptibility and related quantities would help to achieve consistency and avoid confusion in MRI.
John Schenck