Showing papers by "Stony Brook University published in 2015"
TL;DR: The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations, and has reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-generation sequencing, deep exome sequencing, and dense microarray genotyping.
Abstract: The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies.
12,661 citations
TL;DR: Together, these backbone and side chain modifications (hereafter called ff14SB) not only better reproduced their benchmarks, but also improved secondary structure content in small peptides and reproduction of NMR χ1 scalar coupling measurements for proteins in solution.
Abstract: Molecular mechanics is powerful for its speed in atomistic simulations, but an accurate force field is required. The Amber ff99SB force field improved protein secondary structure balance and dynamics from earlier force fields like ff99, but weaknesses in side chain rotamer and backbone secondary structure preferences have been identified. Here, we performed a complete refit of all amino acid side chain dihedral parameters, which had been carried over from ff94. The training set of conformations included multidimensional dihedral scans designed to improve transferability of the parameters. Improvement in all amino acids was obtained as compared to ff99SB. Parameters were also generated for alternate protonation states of ionizable side chains. Average errors in relative energies of pairs of conformations were under 1.0 kcal/mol as compared to QM, reduced 35% from ff99SB. We also took the opportunity to make empirical adjustments to the protein backbone dihedral parameters as compared to ff99SB. Multiple sm...
6,367 citations
TL;DR: The experimental implementation of transistor-free metal-oxide memristor crossbars, with device variability sufficiently low to allow operation of integrated neural networks, in a simple network: a single-layer perceptron (an algorithm for linear classification).
Abstract: Despite much progress in semiconductor integrated circuit technology, the extreme complexity of the human cerebral cortex, with its approximately 10(14) synapses, makes the hardware implementation of neuromorphic networks with a comparable number of devices exceptionally challenging. To provide comparable complexity while operating much faster and with manageable power dissipation, networks based on circuits combining complementary metal-oxide-semiconductors (CMOSs) and adjustable two-terminal resistive devices (memristors) have been developed. In such circuits, the usual CMOS stack is augmented with one or several crossbar layers, with memristors at each crosspoint. There have recently been notable improvements in the fabrication of such memristive crossbars and their integration with CMOS circuits, including first demonstrations of their vertical integration. Separately, discrete memristors have been used as artificial synapses in neuromorphic networks. Very recently, such experiments have been extended to crossbar arrays of phase-change memristive devices. The adjustment of such devices, however, requires an additional transistor at each crosspoint, and hence these devices are much harder to scale than metal-oxide memristors, whose nonlinear current-voltage curves enable transistor-free operation. Here we report the experimental implementation of transistor-free metal-oxide memristor crossbars, with device variability sufficiently low to allow operation of integrated neural networks, in a simple network: a single-layer perceptron (an algorithm for linear classification). The network can be taught in situ using a coarse-grain variety of the delta rule algorithm to perform the perfect classification of 3 × 3-pixel black/white images into three classes (representing letters). This demonstration is an important step towards much larger and more complex memristive neuromorphic networks.
2,222 citations
TL;DR: At Atomic-scale characterization, supported by theoretical calculations, revealed structures reminiscent of fused boron clusters with multiple scales of anisotropic, out-of-plane buckling that are consistent with predictions of a highly an isotropic, 2D metal.
Abstract: At the atomic-cluster scale, pure boron is markedly similar to carbon, forming simple planar molecules and cage-like fullerenes. Theoretical studies predict that two-dimensional (2D) boron sheets will adopt an atomic configuration similar to that of boron atomic clusters. We synthesized atomically thin, crystalline 2D boron sheets (i.e., borophene) on silver surfaces under ultrahigh-vacuum conditions. Atomic-scale characterization, supported by theoretical calculations, revealed structures reminiscent of fused boron clusters with multiple scales of anisotropic, out-of-plane buckling. Unlike bulk boron allotropes, borophene shows metallic characteristics that are consistent with predictions of a highly anisotropic, 2D metal.
1,873 citations
TL;DR: A measurement of the Higgs boson mass is presented based on the combined data samples of the ATLAS and CMS experiments at the CERN LHC in the H→γγ and H→ZZ→4ℓ decay channels.
Abstract: A measurement of the Higgs boson mass is presented based on the combined data samples of the ATLAS and CMS experiments at the CERN LHC in the H→γγ and H→ZZ→4l decay channels. The results are obtained from a simultaneous fit to the reconstructed invariant mass peaks in the two channels and for the two experiments. The measured masses from the individual channels and the two experiments are found to be consistent among themselves. The combined measured mass of the Higgs boson is mH=125.09±0.21 (stat)±0.11 (syst) GeV.
1,567 citations
Royal Netherlands Academy of Arts and Sciences1, Cold Spring Harbor Laboratory2, Lustgarten Foundation3, Stony Brook University4, Watson School of Biological Sciences5, University Medical Center Utrecht6, Utrecht University7, Memorial Sloan Kettering Cancer Center8, Johns Hopkins University School of Medicine9
TL;DR: Comprehensive transcriptional and proteomic analyses of murine pancreatic organoids revealed genes and pathways altered during disease progression that demonstrate that organoids are a facile model system to discover characteristics of this deadly malignancy.
1,488 citations
TL;DR: The wellbeing of elderly people is an important objective for both economic and health policy and present new analyses about the pattern of wellbeing across ages and the association between wellbeing and survival at older ages.
1,334 citations
SLAC National Accelerator Laboratory1, Stockholm University2, Santa Cruz Institute for Particle Physics3, Istituto Nazionale di Fisica Nucleare4, University of Wisconsin-Madison5, Goddard Space Flight Center6, University of Montpellier7, École Polytechnique8, INAF9, George Mason University10, University of Padua11, Instituto Politécnico Nacional12, Fermilab13, C. N. Yang Institute for Theoretical Physics14, Hiroshima University15, Paris Diderot University16, University of Göttingen17, University of North Florida18, University of Iceland19, Spanish National Research Council20, University of Maryland, College Park21, University of California, Irvine22, University of Denver23, Stony Brook University24, Texas A&M University25, Ohio State University26, United States Naval Research Laboratory27
TL;DR: In this article, the authors report on γ-ray observations of the Milky-Way satellite galaxies (dSphs) based on six years of Fermi Large Area Telescope data processed with the new Pass8 event-level analysis.
Abstract: The dwarf spheroidal satellite galaxies (dSphs) of the Milky Way are some of the most dark matter (DM) dominated objects known. We report on γ-ray observations of Milky Way dSphs based on six years of Fermi Large Area Telescope data processed with the new Pass8 event-level analysis. None of the dSphs are significantly detected in γ rays, and we present upper limits on the DM annihilation cross section from a combined analysis of 15 dSphs. These constraints are among the strongest and most robust to date and lie below the canonical thermal relic cross section for DM of mass ≲100 GeV annihilating via quark and τ-lepton channels.
1,166 citations
TL;DR: This work provides a worked example of spatial thinning of species occurrence records for the Caribbean spiny pocket mouse, where the results obtained match those of manual thinning.
Abstract: Spatial thinning of species occurrence records can help address problems associated with spatial sampling biases. Ideally, thinning removes the fewest records necessary to substantially reduce the effects of sampling bias, while simultaneously retaining the greatest amount of useful information. Spatial thinning can be done manually; however, this is prohibitively time consuming for large datasets. Using a randomization approach, the ‘thin’ function in the spThin R package returns a dataset with the maximum number of records for a given thinning distance, when run for sufficient iterations. We here provide a worked example for the Caribbean spiny pocket mouse, where the results obtained match those of manual thinning.
1,016 citations
TL;DR: This survey aims to provide a general, comprehensive, and structured overview of the state-of-the-art methods for anomaly detection in data represented as graphs, and gives a general framework for the algorithms categorized under various settings.
Abstract: Detecting anomalies in data is a vital task, with numerous high-impact applications in areas such as security, finance, health care, and law enforcement. While numerous techniques have been developed in past years for spotting outliers and anomalies in unstructured collections of multi-dimensional points, with graph data becoming ubiquitous, techniques for structured graph data have been of focus recently. As objects in graphs have long-range correlations, a suite of novel technology has been developed for anomaly detection in graph data. This survey aims to provide a general, comprehensive, and structured overview of the state-of-the-art methods for anomaly detection in data represented as graphs. As a key contribution, we give a general framework for the algorithms categorized under various settings: unsupervised versus (semi-)supervised approaches, for static versus dynamic graphs, for attributed versus plain graphs. We highlight the effectiveness, scalability, generality, and robustness aspects of the methods. What is more, we stress the importance of anomaly attribution and highlight the major techniques that facilitate digging out the root cause, or the `why', of the detected anomalies for further analysis and sense-making. Finally, we present several real-world applications of graph-based anomaly detection in diverse domains, including financial, auction, computer traffic, and social networks. We conclude our survey with a discussion on open theoretical and practical challenges in the field.
998 citations
TL;DR: It is found that screen time is adversely associated with sleep outcomes in 90% of studies, and youth should be advised to limit or reduce screen time exposure, especially before or during bedtime hours to minimize any harmful effects of screen time on sleep and well-being.
Paris Descartes University1, Institut Gustave Roussy2, Mount Sinai Hospital3, University of Texas Southwestern Medical Center4, University of Kiel5, Thomas Jefferson University6, Seconda Università degli Studi di Napoli7, University of Toronto8, University of Massachusetts Medical School9, Louisiana State University10, Flanders Institute for Biotechnology11, Ghent University12, Cancer Research UK13, Queen Mary University of London14, Roswell Park Cancer Institute15, Karolinska Institutet16, University of Freiburg17, University of California, San Francisco18, Buck Institute for Research on Aging19, French Institute of Health and Medical Research20, Université Paris-Saclay21, University College London22, University of Rome Tor Vergata23, Northwestern University24, Memorial Sloan Kettering Cancer Center25, National Institutes of Health26, Technion – Israel Institute of Technology27, Johns Hopkins University28, University of Chieti-Pescara29, University of Ulm30, Genentech31, New York University32, Pennsylvania State University33, University of Salento34, Yale University35, Goethe University Frankfurt36, University of Burgundy37, Pasteur Institute38, University of Strasbourg39, University of Zurich40, University of Tokyo41, Technische Universität München42, University of Bern43, University of Michigan44, Medical Research Council45, University of South Australia46, University of Adelaide47, Medical University of South Carolina48, University of Texas at Dallas49, Howard Hughes Medical Institute50, St. John's University51, University of Oviedo52, University of Graz53, Istituto Superiore di Sanità54, Katholieke Universiteit Leuven55, Trinity College, Dublin56, University of Geneva57, University of Amsterdam58, Stony Brook University59, University of Washington60, University of Ferrara61, Royal College of Surgeons in Ireland62, La Trobe University63, University of Buenos Aires64, University of Virginia65, University of Padua66, University of Lisbon67, University of Cambridge68, University of Würzburg69, Soochow University (Suzhou)70, Columbia University71, University of Glasgow72, University of Crete73, Foundation for Research & Technology – Hellas74, Innsbruck Medical University75, Carlos III Health Institute76, Rutgers University77, University of Minnesota78, Harvard University79, City University of New York80, Moscow State University81
TL;DR: The Nomenclature Committee on Cell Death formulates a set of recommendations to help scientists and researchers to discriminate between essential and accessory aspects of cell death.
Abstract: Cells exposed to extreme physicochemical or mechanical stimuli die in an uncontrollable manner, as a result of their immediate structural breakdown. Such an unavoidable variant of cellular demise is generally referred to as ‘accidental cell death’ (ACD). In most settings, however, cell death is initiated by a genetically encoded apparatus, correlating with the fact that its course can be altered by pharmacologic or genetic interventions. ‘Regulated cell death’ (RCD) can occur as part of physiologic programs or can be activated once adaptive responses to perturbations of the extracellular or intracellular microenvironment fail. The biochemical phenomena that accompany RCD may be harnessed to classify it into a few subtypes, which often (but not always) exhibit stereotyped morphologic features. Nonetheless, efficiently inhibiting the processes that are commonly thought to cause RCD, such as the activation of executioner caspases in the course of apoptosis, does not exert true cytoprotective effects in the mammalian system, but simply alters the kinetics of cellular demise as it shifts its morphologic and biochemical correlates. Conversely, bona fide cytoprotection can be achieved by inhibiting the transduction of lethal signals in the early phases of the process, when adaptive responses are still operational. Thus, the mechanisms that truly execute RCD may be less understood, less inhibitable and perhaps more homogeneous than previously thought. Here, the Nomenclature Committee on Cell Death formulates a set of recommendations to help scientists and researchers to discriminate between essential and accessory aspects of cell death.
Sapienza University of Rome1, International Union for Conservation of Nature and Natural Resources2, University of the Witwatersrand3, Microsoft4, Wildlife Conservation Society5, University of Queensland6, BirdLife International7, Norwegian Polar Institute8, James Cook University9, Conservation International10, Commonwealth Scientific and Industrial Research Organisation11, Stony Brook University12, Chinese Academy of Sciences13, Durham University14, National University of Singapore15, University of Melbourne16, Stellenbosch University17, Zoological Society of London18, University College London19, NatureServe20
TL;DR: In this article, three main approaches used to derive these currencies (correlative, mechanistic and trait-based) and their associated data requirements, spatial and temporal scales of application and modelling methods are described.
Abstract: The effects of climate change on biodiversity are increasingly well documented, and many methods have been developed to assess species' vulnerability to climatic changes, both ongoing and projected in the coming decades. To minimize global biodiversity losses, conservationists need to identify those species that are likely to be most vulnerable to the impacts of climate change. In this Review, we summarize different currencies used for assessing species' climate change vulnerability. We describe three main approaches used to derive these currencies (correlative, mechanistic and trait-based), and their associated data requirements, spatial and temporal scales of application and modelling methods. We identify strengths and weaknesses of the approaches and highlight the sources of uncertainty inherent in each method that limit projection reliability. Finally, we provide guidance for conservation practitioners in selecting the most appropriate approach(es) for their planning needs and highlight priority areas for further assessments.
TL;DR: The authors found strong support for the expressive model: a multi-item partisan identity scale better accounts for campaign activity than a strong stance on subjectively important policy issues, the strength of ideological self-placement, or a measure of ideological identity.
Abstract: Party identification is central to the study of American political behavior, yet there remains disagreement over whether it is largely instrumental or expressive in nature. We draw on social identity theory to develop the expressive model and conduct four studies to compare it to an instrumental explanation of campaign involvement. We find strong support for the expressive model: a multi-item partisan identity scale better accounts for campaign activity than a strong stance on subjectively important policy issues, the strength of ideological self-placement, or a measure of ideological identity. A series of experiments underscore the power of partisan identity to generate action-oriented emotions that drive campaign activity. Strongly identified partisans feel angrier than weaker partisans when threatened with electoral loss and more positive when reassured of victory. In contrast, those who hold a strong and ideologically consistent position on issues are no more aroused emotionally than others by party threats or reassurances. In addition, threat and reassurance to the party's status arouse greater anger and enthusiasm among partisans than does a threatened loss or victory on central policy issues. Our findings underscore the power of an expressive partisan identity to drive campaign involvement and generate strong emotional reactions to ongoing campaign events.
TL;DR: It is found that cod stocks declined continuously during intense warming in the North Atlantic, and managing fisheries in a warming world is going to be increasingly problematic.
Abstract: Several studies have documented fish populations changing in response to long-term warming. Over the past decade, sea surface temperatures in the Gulf of Maine increased faster than 99% of the global ocean. The warming, which was related to a northward shift in the Gulf Stream and to changes in the Atlantic Multidecadal Oscillation and Pacific Decadal Oscillation, led to reduced recruitment and increased mortality in the region’s Atlantic cod (Gadus morhua) stock. Failure to recognize the impact of warming on cod contributed to overfishing. Recovery of this fishery depends on sound management, but the size of the stock depends on future temperature conditions. The experience in the Gulf of Maine highlights the need to incorporate environmental factors into resource management.
TL;DR: The discovery of Lomekwi 3 is reported, a 3.3-million-year-old archaeological site where in situ stone artefacts occur in spatiotemporal association with Pliocene hominin fossils in a wooded palaeoenvironment and the name ‘Lomekwian’ is proposed, which predates the Oldowan by 700,000 years and marks a new beginning to the known archaeological record.
Abstract: Human evolutionary scholars have long supposed that the earliest stone tools were made by the genus Homo and that this technological development was directly linked to climate change and the spread of savannah grasslands. New fieldwork in West Turkana, Kenya, has identified evidence of much earlier hominin technological behaviour. We report the discovery of Lomekwi 3, a 3.3-million-year-old archaeological site where in situ stone artefacts occur in spatiotemporal association with Pliocene hominin fossils in a wooded palaeoenvironment. The Lomekwi 3 knappers, with a developing understanding of stone's fracture properties, combined core reduction with battering activities. Given the implications of the Lomekwi 3 assemblage for models aiming to converge environmental change, hominin evolution and technological origins, we propose for it the name 'Lomekwian', which predates the Oldowan by 700,000 years and marks a new beginning to the known archaeological record.
TL;DR: A programmatic line of research indicating that apparent negativity in feedback actually reflects a reward-related positivity (RewP) that is absent or suppressed following nonreward is reviewed.
Abstract: Feedback indicating monetary loss elicits an apparent negative deflection in the event-related potential (ERP) that has been referred to as the feedback error-related negativity, medial frontal negativity, feedback-related negativity, and feedback negativity-all conceptualizations that suggest a negative ERP component that is greater for loss than gain. In the current paper, I review a programmatic line of research indicating that this apparent negativity actually reflects a reward-related positivity (RewP) that is absent or suppressed following nonreward. I situate the RewP within a broader nomological network of reward processing and individual differences in sensitivity to rewards. Further, I review work linking reductions in the RewP to increased depressive symptoms and risk for depression. Finally, I discuss future directions for research on the RewP.
TL;DR: The newly discovered dehydrated Na2-δMnHFC phase exhibits superior electrochemical performance compared to other reported Na-ion cathode materials and delivers at 3.5 V a reversible capacity in a sodium half cell and 140 mAh g(-1) in a full cell with a hard-carbon anode.
Abstract: Sodium is globally available, which makes a sodium-ion rechargeable battery preferable to a lithium-ion battery for large-scale storage of electrical energy, provided a host cathode for Na can be found that provides the necessary capacity, voltage, and cycle life at the prescribed charge/discharge rate. Low-cost hexacyanometallates are promising cathodes because of their ease of synthesis and rigid open framework that enables fast Na+ insertion and extraction. Here we report an intriguing effect of interstitial H2O on the structure and electrochemical properties of sodium manganese(II) hexacyanoferrates(II) with the nominal composition Na2MnFe(CN)6·zH2O (Na2−δMnHFC). The newly discovered dehydrated Na2−δMnHFC phase exhibits superior electrochemical performance compared to other reported Na-ion cathode materials; it delivers at 3.5 V a reversible capacity of 150 mAh g–1 in a sodium half cell and 140 mAh g–1 in a full cell with a hard-carbon anode. At a charge/discharge rate of 20 C, the half-cell capacity ...
Lawrence Livermore National Laboratory1, Stanford University2, University of California, Berkeley3, University of Arizona4, University of California, San Diego5, Ames Research Center6, University of Victoria7, Herzberg Institute of Astrophysics8, Space Telescope Science Institute9, Arizona State University10, Université de Montréal11, Los Alamos National Laboratory12, University of California, Los Angeles13, University of Western Ontario14, Subaru15, University of Hertfordshire16, Princeton University17, University of Toronto18, Centre national de la recherche scientifique19, University of Chicago20, University of California, Santa Cruz21, Durham University22, University of Exeter23, University of Georgia24, Stony Brook University25, University of California, Santa Barbara26, American Museum of Natural History27, University of Chile28, Universities Space Research Association29, Cornell University30, University of Toledo31, California Institute of Technology32
TL;DR: Using the Gemini Planet Imager, a Jupiter-like planet is discovered orbiting the ~20-million-year-old star 51 Eridani at a projected separation of 13 astronomical units and has a methane signature and is probably the smallest exoplanet that has been directly imaged.
Abstract: Directly detecting thermal emission from young extrasolar planets allows measurement of their atmospheric compositions and luminosities, which are influenced by their formation mechanisms. Using the Gemini Planet Imager, we discovered a planet orbiting the ~20-million-year-old star 51 Eridani at a projected separation of 13 astronomical units. Near-infrared observations show a spectrum with strong methane and water-vapor absorption. Modeling of the spectra and photometry yields a luminosity (normalized by the luminosity of the Sun) of 1.6 to 4.0 × 10(-6) and an effective temperature of 600 to 750 kelvin. For this age and luminosity, "hot-start" formation models indicate a mass twice that of Jupiter. This planet also has a sufficiently low luminosity to be consistent with the "cold-start" core-accretion process that may have formed Jupiter.
TL;DR: In this article, a new correspondence between four-dimensional conformal field theories with extended supersymmetry and two-dimensional chiral algebras was described, where the meromorphic correlators of the chiral algebra compute correlators in a protected sector of the fourdimensional theory.
Abstract: We describe a new correspondence between four-dimensional conformal field theories with extended supersymmetry and two-dimensional chiral algebras. The meromorphic correlators of the chiral algebra compute correlators in a protected sector of the four-dimensional theory. Infinite chiral symmetry has far-reaching consequences for the spectral data, correlation functions, and central charges of any four-dimensional theory with $${\mathcal{N}=2}$$
superconformal symmetry.
TL;DR: It is shown, by direct nano-infrared imaging, that these hyperbolic polaritons can be effectively modulated in a van der Waals heterostructure composed of monolayer graphene on h-BN.
Abstract: Hexagonal boron nitride (h-BN) is a natural hyperbolic material, in which the dielectric constants are the same in the basal plane (e(t) ≡ e(x) = e(y)) but have opposite signs (e(t)e(z) < 0) in the normal plane (e(z)). Owing to this property, finite-thickness slabs of h-BN act as multimode waveguides for the propagation of hyperbolic phonon polaritons--collective modes that originate from the coupling between photons and electric dipoles in phonons. However, control of these hyperbolic phonon polaritons modes has remained challenging, mostly because their electrodynamic properties are dictated by the crystal lattice of h-BN. Here we show, by direct nano-infrared imaging, that these hyperbolic polaritons can be effectively modulated in a van der Waals heterostructure composed of monolayer graphene on h-BN. Tunability originates from the hybridization of surface plasmon polaritons in graphene with hyperbolic phonon polaritons in h-BN, so that the eigenmodes of the graphene/h-BN heterostructure are hyperbolic plasmon-phonon polaritons. The hyperbolic plasmon-phonon polaritons in graphene/h-BN suffer little from ohmic losses, making their propagation length 1.5-2.0 times greater than that of hyperbolic phonon polaritons in h-BN. The hyperbolic plasmon-phonon polaritons possess the combined virtues of surface plasmon polaritons in graphene and hyperbolic phonon polaritons in h-BN. Therefore, graphene/h-BN can be classified as an electromagnetic metamaterial as the resulting properties of these devices are not present in its constituent elements alone.
California Institute of Technology1, Imperial College London2, University of California, Santa Cruz3, Indiana University4, University of California, Davis5, Washington University in St. Louis6, United States Geological Survey7, Smithsonian Institution8, University of Tennessee9, Johns Hopkins University10, University of Nantes11, Planetary Science Institute12, Western Washington University13, Ames Research Center14, Goddard Space Flight Center15, University of California, Berkeley16, University of Lyon17, Texas A&M University18, University of Guelph19, Stony Brook University20, University of Texas at Austin21, Brown University22, University of New Mexico23, Los Alamos National Laboratory24
TL;DR: The observations suggest that individual lakes were stable on the ancient surface of Mars for 100 to 10,000 years, a minimum duration when each lake was stable both thermally (as liquid water) and in terms of mass balance (with inputs effectively matching evaporation and loss of water to colder regions).
Abstract: The landforms of northern Gale crater on Mars expose thick sequences of sedimentary rocks. Based on images obtained by the Curiosity rover, we interpret these outcrops as evidence for past fluvial, deltaic, and lacustrine environments. Degradation of the crater wall and rim probably supplied these sediments, which advanced inward from the wall, infilling both the crater and an internal lake basin to a thickness of at least 75 meters. This intracrater lake system probably existed intermittently for thousands to millions of years, implying a relatively wet climate that supplied moisture to the crater rim and transported sediment via streams into the lake basin. The deposits in Gale crater were then exhumed, probably by wind-driven erosion, creating Aeolis Mons (Mount Sharp).
TL;DR: This manuscript presents the latest algorithmic and methodological developments to the structure‐based design program DOCK 6.7 focused on an updated internal energy function, new anchor selection control, enhanced minimization options, a footprint similarity scoring function, a symmetry‐corrected root‐mean‐square deviation algorithm, a database filter, and docking forensic tools.
Abstract: This manuscript presents the latest algorithmic and methodological developments to the structure-based design program DOCK 6.7 focused on an updated internal energy function, new anchor selection control, enhanced minimization options, a footprint similarity scoring function, a symmetry-corrected root-mean-square deviation algorithm, a database filter, and docking forensic tools. An important strategy during development involved use of three orthogonal metrics for assessment and validation: pose reproduction over a large database of 1043 protein-ligand complexes (SB2012 test set), cross-docking to 24 drug-target protein families, and database enrichment using large active and decoy datasets (Directory of Useful Decoys [DUD]-E test set) for five important proteins including HIV protease and IGF-1R. Relative to earlier versions, a key outcome of the work is a significant increase in pose reproduction success in going from DOCK 4.0.2 (51.4%) → 5.4 (65.2%) → 6.7 (73.3%) as a result of significant decreases in failure arising from both sampling 24.1% → 13.6% → 9.1% and scoring 24.4% → 21.1% → 17.5%. Companion cross-docking and enrichment studies with the new version highlight other strengths and remaining areas for improvement, especially for systems containing metal ions. The source code for DOCK 6.7 is available for download and free for academic users at http://dock.compbio.ucsf.edu/.
TL;DR: A survey on indoor wireless tracking of mobile nodes from a signal processing perspective and it can be argued that the indoor tracking problem is more challenging than the problem on indoor localization.
Abstract: In the last decade, the research on and the technology for outdoor tracking have seen an explosion of advances. It is expected that in the near future, we will witness similar trends for indoor scenarios where people spend more than 70% of their lives. The rationale for this is that there is a need for reliable and high-definition real-time tracking systems that have the ability to operate in indoor environments, thus complementing those based on satellite technologies, such as the Global Positioning System (GPS). The indoor environments are very challenging, and as a result, a large variety of technologies have been proposed for coping with them, but no legacy solution has emerged. This paper presents a survey on indoor wireless tracking of mobile nodes from a signal processing perspective. It can be argued that the indoor tracking problem is more challenging than the problem on indoor localization. The reason is simple: From a set of measurements, one has to estimate not one location but a series of correlated locations of a mobile node. The paper illustrates the theory, the main tools, and the most promising technologies for indoor tracking. New directions of research are also discussed.
TL;DR: In this article, the results from six different IceCube searches for astrophysical neutrinos in a maximum-likelihood analysis are combined, and the combined event sample features high-statistics samples of shower-like and track-like events.
Abstract: Evidence for an extraterrestrial flux of high-energy neutrinos has now been found in multiple searches with the IceCube detector. The first solid evidence was provided by a search for neutrino events with deposited energies greater than or similar to 30 TeV and interaction vertices inside the instrumented volume. Recent analyses suggest that the extraterrestrial flux extends to lower energies and is also visible with throughgoing, nu(mu)-induced tracks from the Northern Hemisphere. Here, we combine the results from six different IceCube searches for astrophysical neutrinos in a maximum-likelihood analysis. The combined event sample features high-statistics samples of shower-like and track-like events. The data are fit in up to three observables: energy, zenith angle, and event topology. Assuming the astrophysical neutrino flux to be isotropic and to consist of equal flavors at Earth, the all-flavor spectrum with neutrino energies between 25 TeV and 2.8 PeV is well described by an unbroken power law with best-fit spectral index -2.50 +/- 0.09 and a flux at 100 TeV of (6.7(-1.2)(+1.1)) x 10(-18) GeV-1 s(-1) sr(-1) cm(-2). Under the same assumptions, an unbroken power law with index -2 is disfavored with a significance of 3.8 sigma (p = 0.0066%) with respect to the best fit. This significance is reduced to 2.1 sigma (p = 1.7%) if instead we compare the best fit to a spectrum with index -2 that has an exponential cut-off at high energies. Allowing the electron-neutrino flux to deviate from the other two flavors, we find a nu(e) fraction of 0.18 +/- 0.11 at Earth. The sole production of electron neutrinos, which would be characteristic of neutron-decay-dominated sources, is rejected with a significance of 3.6 sigma ( p = 0.014%).
TL;DR: The study suggests that this new function of autophagy acts as a guarding mechanism protecting cells from tumorigenesis, and prevents activated RAS-induced lamin B1 loss and attenuates oncogene-induced senescence in primary human cells.
Abstract: Macroautophagy (hereafter referred to as autophagy) is a catabolic membrane trafficking process that degrades a variety of cellular constituents and is associated with human diseases. Although extensive studies have focused on autophagic turnover of cytoplasmic materials, little is known about the role of autophagy in degrading nuclear components. Here we report that the autophagy machinery mediates degradation of nuclear lamina components in mammals. The autophagy protein LC3/Atg8, which is involved in autophagy membrane trafficking and substrate delivery, is present in the nucleus and directly interacts with the nuclear lamina protein lamin B1, and binds to lamin-associated domains on chromatin. This LC3-lamin B1 interaction does not downregulate lamin B1 during starvation, but mediates its degradation upon oncogenic insults, such as by activated RAS. Lamin B1 degradation is achieved by nucleus-to-cytoplasm transport that delivers lamin B1 to the lysosome. Inhibiting autophagy or the LC3-lamin B1 interaction prevents activated RAS-induced lamin B1 loss and attenuates oncogene-induced senescence in primary human cells. Our study suggests that this new function of autophagy acts as a guarding mechanism protecting cells from tumorigenesis.
TL;DR: Comparisons to liposomal formulations revealed the significance of the innate immune system along with the complement protein C5 on exosomes' rate of clearance and biodistribution, and limits their use as an anti-cancer drug delivery vehicle.
University of Leeds1, University of Toronto2, Stony Brook University3, University of Essex4, Pacific Northwest National Laboratory5, University of Denver6, University of British Columbia7, University of Manchester8, Fisheries and Oceans Canada9, Environment Canada10, Leibniz Institute for Baltic Sea Research11
TL;DR: It is shown that organic material in the sea surface microlayer nucleates ice under conditions relevant for mixed-phase cloud and high-altitude ice cloud formation, and suggested that marine organic material may be an important source of ice-nucleating particles in remote marine environments.
Abstract: The amount of ice present in clouds can affect cloud lifetime, precipitation and radiative properties. The formation of ice in clouds is facilitated by the presence of airborne ice-nucleating particles. Sea spray is one of the major global sources of atmospheric particles, but it is unclear to what extent these particles are capable of nucleating ice. Sea-spray aerosol contains large amounts of organic material that is ejected into the atmosphere during bubble bursting at the organically enriched sea-air interface or sea surface microlayer. Here we show that organic material in the sea surface microlayer nucleates ice under conditions relevant for mixed-phase cloud and high-altitude ice cloud formation. The ice-nucleating material is probably biogenic and less than approximately 0.2 micrometres in size. We find that exudates separated from cells of the marine diatom Thalassiosira pseudonana nucleate ice, and propose that organic material associated with phytoplankton cell exudates is a likely candidate for the observed ice-nucleating ability of the microlayer samples. Global model simulations of marine organic aerosol, in combination with our measurements, suggest that marine organic material may be an important source of ice-nucleating particles in remote marine environments such as the Southern Ocean, North Pacific Ocean and North Atlantic Ocean.
TL;DR: In this paper, the authors provide an elementary introduction into the physics of anomalous chiral effects, to describe the current status of experimental studies in heavy ion physics, and outline the future work, both in experiment and theory, needed to eliminate the existing uncertainties in the interpretation of the data.
Abstract: The interplay of quantum anomalies with magnetic field and vorticity results in a variety of novel non-dissipative transport phenomena in systems with chiral fermions, including the quark-gluon plasma. Among them is the Chiral Magnetic Effect (CME) -- the generation of electric current along an external magnetic field induced by chirality imbalance. Because the chirality imbalance is related to the global topology of gauge fields, the CME current is topologically protected and hence non-dissipative even in the presence of strong interactions. As a result, the CME and related quantum phenomena affect the hydrodynamical and transport behavior of strongly coupled quark-gluon plasma, and can be studied in relativistic heavy ion collisions where strong magnetic fields are created by the colliding ions. Evidence for the CME and related phenomena has been reported by the STAR Collaboration at Relativistic Heavy Ion Collider at BNL, and by the ALICE Collaboration at the Large Hadron Collider at CERN. The goal of the present review is to provide an elementary introduction into the physics of anomalous chiral effects, to describe the current status of experimental studies in heavy ion physics, and to outline the future work, both in experiment and theory, needed to eliminate the existing uncertainties in the interpretation of the data.
TL;DR: The electronic structure of phagraphene has distorted Dirac cones, which are lower in energy than most of the predicted 2D carbon allotropes due to its sp(2)-binding features and density of atomic packing comparable to graphene.
Abstract: Using systematic evolutionary structure searching we propose a new carbon allotrope, phagraphene [fae'graefi:n], standing for penta-hexa-hepta-graphene, because the structure is composed of 5-6-7 carbon rings. This two-dimensional (2D) carbon structure is lower in energy than most of the predicted 2D carbon allotropes due to its sp(2)-binding features and density of atomic packing comparable to graphene. More interestingly, the electronic structure of phagraphene has distorted Dirac cones. The direction-dependent cones are further proved to be robust against external strain with tunable Fermi velocities.