Showing papers by "University of Maryland, College Park published in 2012"

Fast gapped-read alignment with Bowtie 2

Abstract: As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice across a Large Model Space

Abstract: Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d(N)/d(S) rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

Abstract: Recent advances in high-throughput cDNA sequencing (RNA-seq) can reveal new genes and splice variants and quantify expression genome-wide in a single assay. The volume and complexity of data from RNA-seq experiments necessitate scalable, fast and mathematically principled analysis software. TopHat and Cufflinks are free, open-source software tools for gene discovery and comprehensive expression analysis of high-throughput mRNA sequencing (RNA-seq) data. Together, they allow biologists to identify new genes and new splice variants of known ones, as well as compare gene and transcript expression under two or more conditions. This protocol describes in detail how to use TopHat and Cufflinks to perform such analyses. It also covers several accessory tools and utilities that aid in managing data, including CummeRbund, a tool for visualizing RNA-seq analysis results. Although the procedure assumes basic informatics skills, these tools assume little to no background with RNA-seq analysis and are meant for novices and experts alike. The protocol begins with raw sequencing reads and produces a transcriptome assembly, lists of differentially expressed and regulated genes and transcripts, and publication-quality visualizations of analysis results. The protocol's execution time depends on the volume of transcriptome sequencing data and available computing resources but takes less than 1 d of computer time for typical experiments and ∼1 h of hands-on time.

Structure, function and diversity of the healthy human microbiome

Abstract: The Human Microbiome Project Consortium reports the first results of their analysis of microbial communities from distinct, clinically relevant body habitats in a human cohort; the insights into the microbial communities of a healthy population lay foundations for future exploration of the epidemiology, ecology and translational applications of the human microbiome.

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.

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

Abstract: Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.

Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles.

Abstract: While the quality of the current CHARMM22/CMAP additive force field for proteins has been demonstrated in a large number of applications, limitations in the model with respect to the equilibrium between the sampling of helical and extended conformations in folding simulations have been noted. To overcome this, as well as make other improvements in the model, we present a combination of refinements that should result in enhanced accuracy in simulations of proteins. The common (non Gly, Pro) backbone CMAP potential has been refined against experimental solution NMR data for weakly structured peptides, resulting in a rebalancing of the energies of the α-helix and extended regions of the Ramachandran map, correcting the α-helical bias of CHARMM22/CMAP. The Gly and Pro CMAPs have been refitted to more accurate quantum-mechanical energy surfaces. Side-chain torsion parameters have been optimized by fitting to backbone-dependent quantum-mechanical energy surfaces, followed by additional empirical optimization targeting NMR scalar couplings for unfolded proteins. A comprehensive validation of the revised force field was then performed against data not used to guide parametrization: (i) comparison of simulations of eight proteins in their crystal environments with crystal structures; (ii) comparison with backbone scalar couplings for weakly structured peptides; (iii) comparison with NMR residual dipolar couplings and scalar couplings for both backbone and side-chains in folded proteins; (iv) equilibrium folding of mini-proteins. The results indicate that the revised CHARMM 36 parameters represent an improved model for the modeling and simulation studies of proteins, including studies of protein folding, assembly and functionally relevant conformational changes.

A framework for human microbiome research

Abstract: A variety of microbial communities and their genes (microbiome) exist throughout the human body, playing fundamental roles in human health and disease. The NIH funded Human Microbiome Project (HMP) Consortium has established a population-scale framework which catalyzed significant development of metagenomic protocols resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 to 18 body sites up to three times, which to date, have generated 5,177 microbial taxonomic profiles from 16S rRNA genes and over 3.5 Tb of metagenomic sequence. In parallel, approximately 800 human-associated reference genomes have been sequenced. Collectively, these data represent the largest resource to date describing the abundance and variety of the human microbiome, while providing a platform for current and future studies.

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.

Fermi Large Area Telescope Second Source Catalog

Abstract: We present the second catalog of high-energy γ-ray sources detected by the Large Area Telescope (LAT), the primary science instrument on the Fermi Gamma-ray Space Telescope (Fermi), derived from data taken during the first 24 months of the science phase of the mission, which began on 2008 August 4. Source detection is based on the average flux over the 24 month period. The second Fermi-LAT catalog (2FGL) includes source location regions, defined in terms of elliptical fits to the 95% confidence regions and spectral fits in terms of power-law, exponentially cutoff power-law, or log-normal forms. Also included are flux measurements in five energy bands and light curves on monthly intervals for each source. Twelve sources in the catalog are modeled as spatially extended. We provide a detailed comparison of the results from this catalog with those from the first Fermi-LAT catalog (1FGL). Although the diffuse Galactic and isotropic models used in the 2FGL analysis are improved compared to the 1FGL catalog, we attach caution flags to 162 of the sources to indicate possible confusion with residual imperfections in the diffuse model. The 2FGL catalog contains 1873 sources detected and characterized in the 100 MeV to 100 GeV range of which we consider 127 as being firmly identified and 1171 as being reliably associated with counterparts of known or likely γ-ray-producing source classes.

Estimated carbon dioxide emissions from tropical deforestation improved by carbon-density maps

Abstract: Deforestation contributes 6–17% of anthropogenic carbon dioxide emissions. However, much uncertainty in the calculation of deforestation emissions stems from the inadequacy of forest carbon-density and deforestation data. Now an analysis provides the most-detailed estimate so far of the carbon density of vegetation and the associated carbon dioxide emissions from deforestation for ecosystems across the tropics.

Butterfly genome reveals promiscuous exchange of mimicry adaptations among species

Abstract: Sequencing of the genome of the butterfly Heliconius melpomene shows that closely related Heliconius species exchange protective colour-pattern genes promiscuously.

Hybrid error correction and de novo assembly of single-molecule sequencing reads

Abstract: Single-molecule sequencing instruments can generate multikilobase sequences with the potential to greatly improve genome and transcriptome assembly. However, the error rates of single-molecule reads are high, which has limited their use thus far to resequencing bacteria. To address this limitation, we introduce a correction algorithm and assembly strategy that uses short, high-fidelity sequences to correct the error in single-molecule sequences. We demonstrate the utility of this approach on reads generated by a PacBio RS instrument from phage, prokaryotic and eukaryotic whole genomes, including the previously unsequenced genome of the parrot Melopsittacus undulatus, as well as for RNA-Seq reads of the corn (Zea mays) transcriptome. Our long-read correction achieves >99.9% base-call accuracy, leading to substantially better assemblies than current sequencing strategies: in the best example, the median contig size was quintupled relative to high-coverage, second-generation assemblies. Greater gains are predicted if read lengths continue to increase, including the prospect of single-contig bacterial chromosome assembly.

Does female representation in top management improve firm performance? A panel data investigation

Abstract: We argue that female representation in top management brings informational and social diversity benefits to the top management team, enriches the behaviors exhibited by managers throughout the firm, and motivates women in middle management. The result should be improved managerial task performance and thus better firm performance. We test our theory using 15 years of panel data on the top management teams of the S&P 1,500 firms. We find that female representation in top management improves firm performance but only to the extent that a firm's strategy is focused on innovation, in which context the informational and social benefits of gender diversity and the behaviors associated with women in management are likely to be especially important for managerial task performance. Copyright © 2012 John Wiley & Sons, Ltd.

Psychological Antecedents of Promotive and Prohibitive Voice: A Two-Wave Examination

Abstract: The present study demonstrates how three psychological antecedents (psychological safety, felt obligation for constructive change, and organization-based self-esteem) uniquely, differentially, and interactively predict supervisory reports of promotive and prohibitive “voice” behavior. Using a two-wave panel design, we collected data from a sample of 239 employees to examine the hypothesized relationships. Our results showed that felt obligation was most strongly related to subsequent promotive voice; psychological safety was most strongly related to subsequent prohibitive voice; and organization-based self-esteem was reciprocally related to promotive voice. Further, although felt obligation strengthened the positive effect of psychological safety on both forms of voice, organization-based self-esteem weakened this effect for promotive voice. Theoretical and practical implications are discussed.

The Amazon basin in transition

Abstract: Agricultural expansion and climate variability have become important agents of disturbance in the Amazon basin. Recent studies have demonstrated considerable resilience of Amazonian forests to moderate annual drought, but they also show that interactions between deforestation, fire and drought potentially lead to losses of carbon storage and changes in regional precipitation patterns and river discharge. Although the basin-wide impacts of land use and drought may not yet surpass the magnitude of natural variability of hydrologic and biogeochemical cycles, there are some signs of a transition to a disturbance-dominated regime. These signs include changing energy and water cycles in the southern and eastern portions of the Amazon basin.

Fractionalized excitations in the spin-liquid state of a kagome-lattice antiferromagnet

Abstract: The experimental realization of quantum spin liquids is a long-sought goal in physics, as they represent new states of matter. Quantum spin liquids cannot be described by the broken symmetries associated with conventional ground states. In fact, the interacting magnetic moments in these systems do not order, but are highly entangled with one another over long ranges. Spin liquids have a prominent role in theories describing high-transition-temperature superconductors, and the topological properties of these states may have applications in quantum information. A key feature of spin liquids is that they support exotic spin excitations carrying fractional quantum numbers. However, detailed measurements of these 'fractionalized excitations' have been lacking. Here we report neutron scattering measurements on single-crystal samples of the spin-1/2 kagome-lattice antiferromagnet ZnCu(3)(OD)(6)Cl(2) (also called herbertsmithite), which provide striking evidence for this characteristic feature of spin liquids. At low temperatures, we find that the spin excitations form a continuum, in contrast to the conventional spin waves expected in ordered antiferromagnets. The observation of such a continuum is noteworthy because, so far, this signature of fractional spin excitations has been observed only in one-dimensional systems. The results also serve as a hallmark of the quantum spin-liquid state in herbertsmithite.

Carbon emissions from land use and land-cover change

Abstract: . The net flux of carbon from land use and land-cover change (LULCC) accounted for 12.5% of anthropogenic carbon emissions from 1990 to 2010. This net flux is the most uncertain term in the global carbon budget, not only because of uncertainties in rates of deforestation and forestation, but also because of uncertainties in the carbon density of the lands actually undergoing change. Furthermore, there are differences in approaches used to determine the flux that introduce variability into estimates in ways that are difficult to evaluate, and not all analyses consider the same types of management activities. Thirteen recent estimates of net carbon emissions from LULCC are summarized here. In addition to deforestation, all analyses considered changes in the area of agricultural lands (croplands and pastures). Some considered, also, forest management (wood harvest, shifting cultivation). None included emissions from the degradation of tropical peatlands. Means and standard deviations across the thirteen model estimates of annual emissions for the 1980s and 1990s, respectively, are 1.14 ± 0.23 and 1.12 ± 0.25 Pg C yr−1 (1 Pg = 1015 g carbon). Four studies also considered the period 2000–2009, and the mean and standard deviations across these four for the three decades are 1.14 ± 0.39, 1.17 ± 0.32, and 1.10 ± 0.11 Pg C yr−1. For the period 1990–2009 the mean global emissions from LULCC are 1.14 ± 0.18 Pg C yr−1. The standard deviations across model means shown here are smaller than previous estimates of uncertainty as they do not account for the errors that result from data uncertainty and from an incomplete understanding of all the processes affecting the net flux of carbon from LULCC. Although these errors have not been systematically evaluated, based on partial analyses available in the literature and expert opinion, they are estimated to be on the order of ± 0.5 Pg C yr−1.

Optimal Packet Scheduling in an Energy Harvesting Communication System

Abstract: We consider the optimal packet scheduling problem in a single-user energy harvesting wireless communication system. In this system, both the data packets and the harvested energy are modeled to arrive at the source node randomly. Our goal is to adaptively change the transmission rate according to the traffic load and available energy, such that the time by which all packets are delivered is minimized. Under a deterministic system setting, we assume that the energy harvesting times and harvested energy amounts are known before the transmission starts. For the data traffic arrivals, we consider two different scenarios. In the first scenario, we assume that all bits have arrived and are ready at the transmitter before the transmission starts. In the second scenario, we consider the case where packets arrive during the transmissions, with known arrival times and sizes. We develop optimal off-line scheduling policies which minimize the time by which all packets are delivered to the destination, under causality constraints on both data and energy arrivals.

An Introduction to Gröbner Bases

Abstract: Basic theory of Grobner bases Applications of Grobner bases Modules and Grobner bases Grobner bases over rings Appendix A. Computations and algorithms Appendix B. Well-ordering and induction References List of symbols Index.

A Longitudinal Investigation of the Role of Quantity and Quality of Child-Directed Speech in Vocabulary Development

Abstract: Quantity and quality of caregiver input was examined longitudinally in a sample of 50 parent–child dyads to determine which aspects of input contribute most to children’s vocabulary skill across early development. Measures of input gleaned from parent–child interactions at child ages 18, 30, and 42 months were examined in relation to children’s vocabulary skill on a standardized measure 1 year later (e.g., 30, 42, and 54 months). Results show that controlling for socioeconomic status, input quantity, and children’s previous vocabulary skill; using a diverse and sophisticated vocabulary with toddlers; and using decontextualized language (e.g., narrative) with preschoolers explains additional variation in later vocabulary ability. The differential effects of various aspects of the communicative environment at several points in early vocabulary development are discussed.

Combined results of searches for the standard model Higgs boson in pp collisions at √s = 7 TeV

Abstract: Combined results are reported from searches for the standard model Higgs boson in proton-proton collisions at sqrt(s)=7 TeV in five Higgs boson decay modes: gamma pair, b-quark pair, tau lepton pair, W pair, and Z pair. The explored Higgs boson mass range is 110-600 GeV. The analysed data correspond to an integrated luminosity of 4.6-4.8 inverse femtobarns. The expected excluded mass range in the absence of the standard model Higgs boson is 118-543 GeV at 95% CL. The observed results exclude the standard model Higgs boson in the mass range 127-600 GeV at 95% CL, and in the mass range 129-525 GeV at 99% CL. An excess of events above the expected standard model background is observed at the low end of the explored mass range making the observed limits weaker than expected in the absence of a signal. The largest excess, with a local significance of 3.1 sigma, is observed for a Higgs boson mass hypothesis of 124 GeV. The global significance of observing an excess with a local significance greater than 3.1 sigma anywhere in the search range 110-600 (110-145) GeV is estimated to be 1.5 sigma (2.1 sigma). More data are required to ascertain the origin of this excess.

A Green Vehicle Routing Problem

Abstract: A Green Vehicle Routing Problem (G-VRP) is formulated and solution techniques are developed to aid organizations with alternative fuel-powered vehicle fleets in overcoming difficulties that exist as a result of limited vehicle driving range in conjunction with limited refueling infrastructure The G-VRP is formulated as a mixed integer linear program Two construction heuristics, the Modified Clarke and Wright Savings heuristic and the Density-Based Clustering Algorithm, and a customized improvement technique, are developed Results of numerical experiments show that the heuristics perform well Moreover, problem feasibility depends on customer and station location configurations Implications of technology adoption on operations are discussed

Warming experiments underpredict plant phenological responses to climate change

Abstract: Warming experiments are increasingly relied on to estimate plant responses to global climate change. For experiments to provide meaningful predictions of future responses, they should reflect the empirical record of responses to temperature variability and recent warming, including advances in the timing of flowering and leafing. We compared phenology (the timing of recurring life history events) in observational studies and warming experiments spanning four continents and 1,634 plant species using a common measure of temperature sensitivity (change in days per degree Celsius). We show that warming experiments underpredict advances in the timing of flowering and leafing by 8.5-fold and 4.0-fold, respectively, compared with long-term observations. For species that were common to both study types, the experimental results did not match the observational data in sign or magnitude. The observational data also showed that species that flower earliest in the spring have the highest temperature sensitivities, but this trend was not reflected in the experimental data. These significant mismatches seem to be unrelated to the study length or to the degree of manipulated warming in experiments. The discrepancy between experiments and observations, however, could arise from complex interactions among multiple drivers in the observational data, or it could arise from remediable artefacts in the experiments that result in lower irradiance and drier soils, thus dampening the phenological responses to manipulated warming. Our results introduce uncertainty into ecosystem models that are informed solely by experiments and suggest that responses to climate change that are predicted using such models should be re-evaluated.

GAGE: A critical evaluation of genome assemblies and assembly algorithms

Abstract: New sequencing technology has dramatically altered the landscape of whole-genome sequencing, allowing scientists to initiate numerous projects to decode the genomes of previously unsequenced organisms. The lowest-cost technology can generate deep coverage of most species, including mammals, in just a few days. The sequence data generated by one of these projects consist of millions or billions of short DNA sequences (reads) that range from 50 to 150 nt in length. These sequences must then be assembled de novo before most genome analyses can begin. Unfortunately, genome assembly remains a very difficult problem, made more difficult by shorter reads and unreliable long-range linking information. In this study, we evaluated several of the leading de novo assembly algorithms on four different short-read data sets, all generated by Illumina sequencers. Our results describe the relative performance of the different assemblers as well as other significant differences in assembly difficulty that appear to be inherent in the genomes themselves. Three overarching conclusions are apparent: first, that data quality, rather than the assembler itself, has a dramatic effect on the quality of an assembled genome; second, that the degree of contiguity of an assembly varies enormously among different assemblers and different genomes; and third, that the correctness of an assembly also varies widely and is not well correlated with statistics on contiguity. To enable others to replicate our results, all of our data and methods are freely available, as are all assemblers used in this study.

Modified Newtonian Dynamics (MOND):Observational Phenomenology and Relativistic Extensions

Abstract: A wealth of astronomical data indicate the presence of mass discrepancies in the Universe. The motions observed in a variety of classes of extragalactic systems exceed what can be explained by the mass visible in stars and gas. Either (i) there is a vast amount of unseen mass in some novel form — dark matter — or (ii) the data indicate a breakdown of our understanding of dynamics on the relevant scales, or (iii) both. Here, we first review a few outstanding challenges for the dark matter interpretation of mass discrepancies in galaxies, purely based on observations and independently of any alternative theoretical framework. We then show that many of these puzzling observations are predicted by one single relation — Milgrom’s law — involving an acceleration constant a0 (or a characteristic surface density Σ† = a0/G) on the order of the square-root of the cosmological constant in natural units. This relation can at present most easily be interpreted as the effect of a single universal force law resulting from a modification of Newtonian dynamics (MOND) on galactic scales. We exhaustively review the current observational successes and problems of this alternative paradigm at all astrophysical scales, and summarize the various theoretical attempts (TeVeS, GEA, BIMOND, and others) made to effectively embed this modification of Newtonian dynamics within a relativistic theory of gravity.

Leafsnap: a computer vision system for automatic plant species identification

Abstract: We describe the first mobile app for identifying plant species using automatic visual recognition. The system --- called Leafsnap --- identifies tree species from photographs of their leaves. Key to this system are computer vision components for discarding non-leaf images, segmenting the leaf from an untextured background, extracting features representing the curvature of the leaf's contour over multiple scales, and identifying the species from a dataset of the 184 trees in the Northeastern United States. Our system obtains state-of-the-art performance on the real-world images from the new Leafsnap Dataset --- the largest of its kind. Throughout the paper, we document many of the practical steps needed to produce a computer vision system such as ours, which currently has nearly a million users.