Showing papers by "Max Planck Society published in 2012"

Fiji: an open-source platform for biological-image analysis

Abstract: Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

Abstract: SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. The referred database release 111 (July 2012) contains 3 194 778 small subunit and 288 717 large subunit rRNA gene sequences. Since the initial description of the project, substantial new features have been introduced, including advanced quality control procedures, an improved rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. Furthermore, the extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.

Review of Particle Physics: Particle data group

Abstract: This biennial Review summarizes much of particle physics. Using data from previous editions, plus 2658 new measurements from 644 papers, we list, evaluate, and average measured properties of gauge bosons, leptons, quarks, mesons, and baryons. We summarize searches for hypothetical particles such as Higgs bosons, heavy neutrinos, and supersymmetric particles. All the particle properties and search limits are listed in Summary Tables. We also give numerous tables, figures, formulae, and reviews of topics such as the Standard Model, particle detectors, probability, and statistics. Among the 112 reviews are many that are new or heavily revised including those on Heavy-Quark and Soft-Collinear Effective Theory, Neutrino Cross Section Measurements, Monte Carlo Event Generators, Lattice QCD, Heavy Quarkonium Spectroscopy, Top Quark, Dark Matter, V-cb & V-ub, Quantum Chromodynamics, High-Energy Collider Parameters, Astrophysical Constants, Cosmological Parameters, and Dark Matter. A booklet is available containing the Summary Tables and abbreviated versions of some of the other sections of this full Review. All tables, listings, and reviews (and errata) are also available on the Particle Data Group website: http://pdg.lbl.gov.

Guidelines for the use and interpretation of assays for monitoring autophagy

Abstract: In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.

A kernel two-sample test

Abstract: We propose a framework for analyzing and comparing distributions, which we use to construct statistical tests to determine if two samples are drawn from different distributions. Our test statistic is the largest difference in expectations over functions in the unit ball of a reproducing kernel Hilbert space (RKHS), and is called the maximum mean discrepancy (MMD).We present two distribution free tests based on large deviation bounds for the MMD, and a third test based on the asymptotic distribution of this statistic. The MMD can be computed in quadratic time, although efficient linear time approximations are available. Our statistic is an instance of an integral probability metric, and various classical metrics on distributions are obtained when alternative function classes are used in place of an RKHS. We apply our two-sample tests to a variety of problems, including attribute matching for databases using the Hungarian marriage method, where they perform strongly. Excellent performance is also obtained when comparing distributions over graphs, for which these are the first such tests.

Comprehensive genomic characterization of squamous cell lung cancers

Abstract: Lung squamous cell carcinoma is a common type of lung cancer, causing approximately 400,000 deaths per year worldwide. Genomic alterations in squamous cell lung cancers have not been comprehensively characterized, and no molecularly targeted agents have been specifically developed for its treatment. As part of The Cancer Genome Atlas, here we profile 178 lung squamous cell carcinomas to provide a comprehensive landscape of genomic and epigenomic alterations. We show that the tumour type is characterized by complex genomic alterations, with a mean of 360 exonic mutations, 165 genomic rearrangements, and 323 segments of copy number alteration per tumour. We find statistically recurrent mutations in 11 genes, including mutation of TP53 in nearly all specimens. Previously unreported loss-of-function mutations are seen in the HLA-A class I major histocompatibility gene. Significantly altered pathways included NFE2L2 and KEAP1 in 34%, squamous differentiation genes in 44%, phosphatidylinositol-3-OH kinase pathway genes in 47%, and CDKN2A and RB1 in 72% of tumours. We identified a potential therapeutic target in most tumours, offering new avenues of investigation for the treatment of squamous cell lung cancers.

Pedestrian Detection: An Evaluation of the State of the Art

Abstract: Pedestrian detection is a key problem in computer vision, with several applications that have the potential to positively impact quality of life. In recent years, the number of approaches to detecting pedestrians in monocular images has grown steadily. However, multiple data sets and widely varying evaluation protocols are used, making direct comparisons difficult. To address these shortcomings, we perform an extensive evaluation of the state of the art in a unified framework. We make three primary contributions: 1) We put together a large, well-annotated, and realistic monocular pedestrian detection data set and study the statistics of the size, position, and occlusion patterns of pedestrians in urban scenes, 2) we propose a refined per-frame evaluation methodology that allows us to carry out probing and informative comparisons, including measuring performance in relation to scale and occlusion, and 3) we evaluate the performance of sixteen pretrained state-of-the-art detectors across six data sets. Our study allows us to assess the state of the art and provides a framework for gauging future efforts. Our experiments show that despite significant progress, performance still has much room for improvement. In particular, detection is disappointing at low resolutions and for partially occluded pedestrians.

The Top 10 fungal pathogens in molecular plant pathology

Abstract: The aim of this review was to survey all fungal pathologists with an association with the journal Molecular Plant Pathology and ask them to nominate which fungal pathogens they would place in a 'Top 10' based on scientific/economic importance. The survey generated 495 votes from the international community, and resulted in the generation of a Top 10 fungal plant pathogen list for Molecular Plant Pathology. The Top 10 list includes, in rank order, (1) Magnaporthe oryzae; (2) Botrytis cinerea; (3) Puccinia spp.; (4) Fusarium graminearum; (5) Fusarium oxysporum; (6) Blumeria graminis; (7) Mycosphaerella graminicola; (8) Colletotrichum spp.; (9) Ustilago maydis; (10) Melampsora lini, with honourable mentions for fungi just missing out on the Top 10, including Phakopsora pachyrhizi and Rhizoctonia solani. This article presents a short resume of each fungus in the Top 10 list and its importance, with the intent of initiating discussion and debate amongst the plant mycology community, as well as laying down a bench-mark. It will be interesting to see in future years how perceptions change and what fungi will comprise any future Top 10.

Gaussian quantum information

Abstract: The science of quantum information has arisen over the last two decades centered on the manipulation of individual quanta of information, known as quantum bits or qubits. Quantum computers, quantum cryptography, and quantum teleportation are among the most celebrated ideas that have emerged from this new field. It was realized later on that using continuous-variable quantum information carriers, instead of qubits, constitutes an extremely powerful alternative approach to quantum information processing. This review focuses on continuous-variable quantum information processes that rely on any combination of Gaussian states, Gaussian operations, and Gaussian measurements. Interestingly, such a restriction to the Gaussian realm comes with various benefits, since on the theoretical side, simple analytical tools are available and, on the experimental side, optical components effecting Gaussian processes are readily available in the laboratory. Yet, Gaussian quantum information processing opens the way to a wide variety of tasks and applications, including quantum communication, quantum cryptography, quantum computation, quantum teleportation, and quantum state and channel discrimination. This review reports on the state of the art in this field, ranging from the basic theoretical tools and landmark experimental realizations to the most recent successful developments.

Polymeric Graphitic Carbon Nitride as a Heterogeneous Organocatalyst: From Photochemistry to Multipurpose Catalysis to Sustainable Chemistry

Abstract: Polymeric graphitic carbon nitride materials (for simplicity: g-C(3)N(4)) have attracted much attention in recent years because of their similarity to graphene. They are composed of C, N, and some minor H content only. In contrast to graphenes, g-C(3)N(4) is a medium-bandgap semiconductor and in that role an effective photocatalyst and chemical catalyst for a broad variety of reactions. In this Review, we describe the "polymer chemistry" of this structure, how band positions and bandgap can be varied by doping and copolymerization, and how the organic solid can be textured to make it an effective heterogenous catalyst. g-C(3)N(4) and its modifications have a high thermal and chemical stability and can catalyze a number of "dream reactions", such as photochemical splitting of water, mild and selective oxidation reactions, and--as a coactive catalytic support--superactive hydrogenation reactions. As carbon nitride is metal-free as such, it also tolerates functional groups and is therefore suited for multipurpose applications in biomass conversion and sustainable chemistry.

The tomato genome sequence provides insights into fleshy fruit evolution

Abstract: Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium2, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.

Spatial partitioning of the regulatory landscape of the X-inactivation centre

Abstract: High-order chromatin folding in topologically associating domains has a critical role in proper long-range transcriptional control around the Xist locus, and presumably throughout the genome. The spatial organization of the genome is linked to biological function, and advances in genomic technologies are allowing the conformation of chromosomes to be assessed genome wide. Two groups present complementary papers on the subject. Bing Ren and colleagues use Hi-C, an adaption of the chromosome conformation capture (3C) technique, to investigate the three-dimensional organization of the human and mouse genomes in embryonic stem cells and terminally differentiated cell types. Large, megabase-sized chromatin interaction domains, termed topological domains, are found to be a pervasive and conserved feature of genome organization. Edith Heard and colleagues use chromosome conformation capture carbon-copy (5C) technology and high-resolution microscopy to obtain a high-resolution map of the chromosomal interactions over a large region of the mouse X chromosome, including the X-inactivation centre. A series of discrete topologically associating domains is revealed, as is a previously unknown long intergenic RNA with a potential regulatory role. In eukaryotes transcriptional regulation often involves multiple long-range elements and is influenced by the genomic environment1. A prime example of this concerns the mouse X-inactivation centre (Xic), which orchestrates the initiation of X-chromosome inactivation (XCI) by controlling the expression of the non-protein-coding Xist transcript. The extent of Xic sequences required for the proper regulation of Xist remains unknown. Here we use chromosome conformation capture carbon-copy (5C)2 and super-resolution microscopy to analyse the spatial organization of a 4.5-megabases (Mb) region including Xist. We discover a series of discrete 200-kilobase to 1 Mb topologically associating domains (TADs), present both before and after cell differentiation and on the active and inactive X. TADs align with, but do not rely on, several domain-wide features of the epigenome, such as H3K27me3 or H3K9me2 blocks and lamina-associated domains. TADs also align with coordinately regulated gene clusters. Disruption of a TAD boundary causes ectopic chromosomal contacts and long-range transcriptional misregulation. The Xist/Tsix sense/antisense unit illustrates how TADs enable the spatial segregation of oppositely regulated chromosomal neighbourhoods, with the respective promoters of Xist and Tsix lying in adjacent TADs, each containing their known positive regulators. We identify a novel distal regulatory region of Tsix within its TAD, which produces a long intervening RNA, Linx. In addition to uncovering a new principle of cis-regulatory architecture of mammalian chromosomes, our study sets the stage for the full genetic dissection of the X-inactivation centre.

SINA: accurate high throughput multiple sequence alignment of ribosomal RNA genes

Abstract: Motivation: In the analysis of homologous sequences, computation of multiple sequence alignments (MSAs) has become a bottleneck. This is especially troublesome for marker genes like the ribosomal RNA (rRNA) where already millions of sequences are publicly available and individual studies can easily produce hundreds of thousands of new sequences. Methods have been developed to cope with such numbers, but further improvements are needed to meet accuracy requirements. Results: In this study, we present the SILVA Incremental Aligner (SINA) used to align the rRNA gene databases provided by the SILVA ribosomal RNA project. SINA uses a combination of k-mer searching and partial order alignment (POA) to maintain very high alignment accuracy while satisfying high throughput performance demands. SINA was evaluated in comparison with the commonly used high throughput MSA programs PyNAST and mothur. The three BRAliBase III benchmark MSAs could be reproduced with 99.3, 97.6 and 96.1% accuracy. A larger benchmark MSA comprising 38 772 sequences could be reproduced with 98.9 and 99.3% accuracy using reference MSAs comprising 1000 and 5000 sequences. SINA was able to achieve higher accuracy than PyNAST and mothur in all performed benchmarks. Availability: Alignment of up to 500 sequences using the latest SILVA SSU/LSU Ref datasets as reference MSA is offered at http://www.arb-silva.de/aligner. This page also links to Linux binaries, user manual and tutorial. SINA is made available under a personal use license. Contact: epruesse@mpi-bremen.de Supplementary information: Supplementary data are available at Bioinformatics online.

The clustering of galaxies in the sdss-iii baryon oscillation spectroscopic survey: Baryon acoustic oscillations in the data release 9 spectroscopic galaxy sample

Abstract: We present a one per cent measurement of the cosmic distance scale from the detections of the baryon acoustic oscillations in the clustering of galaxies from the Baryon Oscillation Spectroscopic Survey (BOSS), which is part of the Sloan Digital Sky Survey III (SDSS-III). Our results come from the Data Release 11 (DR11) sample, containing nearly one million galaxies and covering approximately $8\,500$ square degrees and the redshift range $0.2

Emergent phenomena at oxide interfaces

Abstract: Recent technical advances in the atomic-scale synthesis of oxide heterostructures have provided a fertile new ground for creating novel states at their interfaces. Different symmetry constraints can be used to design structures exhibiting phenomena not found in the bulk constituents. A characteristic feature is the reconstruction of the charge, spin and orbital states at interfaces on the nanometre scale. Examples such as interface superconductivity, magneto-electric coupling, and the quantum Hall effect in oxide heterostructures are representative of the scientific and technological opportunities in this rapidly emerging field.

3D Nitrogen-Doped Graphene Aerogel-Supported Fe3O4 Nanoparticles as Efficient Electrocatalysts for the Oxygen Reduction Reaction

Abstract: Three-dimensional (3D) N-doped graphene aerogel (N-GA)-supported Fe3O4 nanoparticles (Fe3O4/N-GAs) as efficient cathode catalysts for the oxygen reduction reaction (ORR) are reported. The graphene hybrids exhibit an interconnected macroporous framework of graphene sheets with uniform dispersion of Fe3O4 nanoparticles (NPs). In studying the effects of the carbon support on the Fe3O4 NPs for the ORR, we found that Fe3O4/N-GAs show a more positive onset potential, higher cathodic density, lower H2O2 yield, and higher electron transfer number for the ORR in alkaline media than Fe3O4 NPs supported on N-doped carbon black or N-doped graphene sheets, highlighting the importance of the 3D macropores and high specific surface area of the GA support for improving the ORR performance. Furthermore, Fe3O4/N-GAs show better durability than the commercial Pt/C catalyst.

Quantum simulations with ultracold quantum gases

Abstract: Experiments with ultracold quantum gases provide a platform for creating many-body systems that can be well controlled and whose parameters can be tuned over a wide range. These properties put these systems in an ideal position for simulating problems that are out of reach for classical computers. This review surveys key advances in this field and discusses the possibilities offered by this approach to quantum simulation.

The Active Site of Methanol Synthesis over Cu/ZnO/Al2O3 Industrial Catalysts

Abstract: Unlike homogeneous catalysts, heterogeneous catalysts that have been optimized through decades are typically so complex and hard to characterize that the nature of the catalytically active site is not known. This is one of the main stumbling blocks in developing rational catalyst design strategies in heterogeneous catalysis. We show here how to identify the crucial atomic structure motif for the industrial Cu/ZnO/Al{sub 2}O{sub 3} methanol synthesis catalyst. Using a combination of experimental evidence from bulk-, surface-sensitive and imaging methods collected on real high-performance catalytic systems in combination with DFT calculations. We show that the active site consists of Cu steps peppered with Zn atoms, all stabilized by a series of well defined bulk defects and surface species that need jointly to be present for the system to work.

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

Abstract: Sequence-based protein function and structure prediction depends crucially on sequence-search sensitivity and accuracy of the resulting sequence alignments. We present an open-source, general-purpose tool that represents both query and database sequences by profile hidden Markov models (HMMs): 'HMM-HMM-based lightning-fast iterative sequence search' (HHblits; http://toolkit.genzentrum.lmu.de/hhblits/). Compared to the sequence-search tool PSI-BLAST, HHblits is faster owing to its discretized-profile prefilter, has 50-100% higher sensitivity and generates more accurate alignments.

Gate-tuning of graphene plasmons revealed by infrared nano-imaging

Abstract: Surface plasmons are collective oscillations of electrons in metals or semiconductors that enable confinement and control of electromagnetic energy at subwavelength scales. Rapid progress in plasmonics has largely relied on advances in device nano-fabrication, whereas less attention has been paid to the tunable properties of plasmonic media. One such medium--graphene--is amenable to convenient tuning of its electronic and optical properties by varying the applied voltage. Here, using infrared nano-imaging, we show that common graphene/SiO(2)/Si back-gated structures support propagating surface plasmons. The wavelength of graphene plasmons is of the order of 200 nanometres at technologically relevant infrared frequencies, and they can propagate several times this distance. We have succeeded in altering both the amplitude and the wavelength of these plasmons by varying the gate voltage. Using plasmon interferometry, we investigated losses in graphene by exploring real-space profiles of plasmon standing waves formed between the tip of our nano-probe and the edges of the samples. Plasmon dissipation quantified through this analysis is linked to the exotic electrodynamics of graphene. Standard plasmonic figures of merit of our tunable graphene devices surpass those of common metal-based structures.

Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota

Abstract: The plant root defines the interface between a multicellular eukaryote and soil, one of the richest microbial ecosystems on Earth. Notably, soil bacteria are able to multiply inside roots as benign endophytes and modulate plant growth and development, with implications ranging from enhanced crop productivity to phytoremediation. Endophytic colonization represents an apparent paradox of plant innate immunity because plant cells can detect an array of microbe-associated molecular patterns (also known as MAMPs) to initiate immune responses to terminate microbial multiplication. Several studies attempted to describe the structure of bacterial root endophytes; however, different sampling protocols and low-resolution profiling methods make it difficult to infer general principles. Here we describe methodology to characterize and compare soil- and root-inhabiting bacterial communities, which reveals not only a function for metabolically active plant cells but also for inert cell-wall features in the selection of soil bacteria for host colonization. We show that the roots of Arabidopsis thaliana, grown in different natural soils under controlled environmental conditions, are preferentially colonized by Proteobacteria, Bacteroidetes and Actinobacteria, and each bacterial phylum is represented by a dominating class or family. Soil type defines the composition of root-inhabiting bacterial communities and host genotype determines their ribotype profiles to a limited extent. The identification of soil-type-specific members within the root-inhabiting assemblies supports our conclusion that these represent soil-derived root endophytes. Surprisingly, plant cell-wall features of other tested plant species seem to provide a sufficient cue for the assembly of approximately 40% of the Arabidopsis bacterial root-inhabiting microbiota, with a bias for Betaproteobacteria. Thus, this root sub-community may not be Arabidopsis-specific but saprophytic bacteria that would naturally be found on any plant root or plant debris in the tested soils. By contrast, colonization of Arabidopsis roots by members of the Actinobacteria depends on other cues from metabolically active host cells.

Fast and Accurate Modeling of Molecular Atomization Energies with Machine Learning

Abstract: We introduce a machine learning model to predict atomization energies of a diverse set of organic molecules, based on nuclear charges and atomic positions only. The problem of solving the molecular Schrodinger equation is mapped onto a nonlinear statistical regression problem of reduced complexity. Regression models are trained on and compared to atomization energies computed with hybrid density- functional theory. Cross validation over more than seven thousand organic molecules yields a mean absolute error of � 10 kcal=mol. Applicability is demonstrated for the prediction of molecular atomization potential energy curves.

A naturalistic open source movie for optical flow evaluation

Abstract: Ground truth optical flow is difficult to measure in real scenes with natural motion As a result, optical flow data sets are restricted in terms of size, complexity, and diversity, making optical flow algorithms difficult to train and test on realistic data We introduce a new optical flow data set derived from the open source 3D animated short film Sintel This data set has important features not present in the popular Middlebury flow evaluation: long sequences, large motions, specular reflections, motion blur, defocus blur, and atmospheric effects Because the graphics data that generated the movie is open source, we are able to render scenes under conditions of varying complexity to evaluate where existing flow algorithms fail We evaluate several recent optical flow algorithms and find that current highly-ranked methods on the Middlebury evaluation have difficulty with this more complex data set suggesting further research on optical flow estimation is needed To validate the use of synthetic data, we compare the image- and flow-statistics of Sintel to those of real films and videos and show that they are similar The data set, metrics, and evaluation website are publicly available

Parity–time synthetic photonic lattices

Abstract: The development of new artificial structures and materials is today one of the major research challenges in optics. In most studies so far, the design of such structures has been based on the judicious manipulation of their refractive index properties. Recently, the prospect of simultaneously using gain and loss was suggested as a new way of achieving optical behaviour that is at present unattainable with standard arrangements. What facilitated these quests is the recently developed notion of 'parity-time symmetry' in optical systems, which allows a controlled interplay between gain and loss. Here we report the experimental observation of light transport in large-scale temporal lattices that are parity-time symmetric. In addition, we demonstrate that periodic structures respecting this symmetry can act as unidirectional invisible media when operated near their exceptional points. Our experimental results represent a step in the application of concepts from parity-time symmetry to a new generation of multifunctional optical devices and networks.

Candle Soot as a Template for a Transparent Robust Superamphiphobic Coating

Abstract: Coating is an essential step in adjusting the surface properties of materials. Superhydrophobic coatings with contact angles greater than 150° and roll-off angles below 10° for water have been developed, based on low-energy surfaces and roughness on the nano- and micrometer scales. However, these surfaces are still wetted by organic liquids such as surfactant-based solutions, alcohols, or alkanes. Coatings that are simultaneously superhydrophobic and superoleophobic are rare. We designed an easily fabricated, transparent, and oil-rebounding superamphiphobic coating. A porous deposit of candle soot was coated with a 25-nanometer-thick silica shell. The black coating became transparent after calcination at 600°C. After silanization, the coating was superamphiphobic and remained so even after its top layer was damaged by sand impingement.

A high-coverage genome sequence from an archaic Denisovan individual

Abstract: We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30×) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity indicating that genetic diversity in these archaic hominins was extremely low. It also allows tentative dating of the specimen on the basis of “missing evolution” in its genome, detailed measurements of Denisovan and Neandertal admixture into present-day human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans.