Showing papers by "University of Maryland, College Park published in 2014"

Composition of the Continental Crust

Abstract: This chapter reviews the present-day composition of the continental crust, the methods employed to derive these estimates, and the implications of the continental crust composition for the formation of the continents, Earth differentiation, and its geochemical inventories. We review the composition of the upper, middle, and lower continental crust. We then examine the bulk crust composition and the implications of this composition for crust generation and modification processes. Finally, we compare the Earth's crust with those of the other terrestrial planets in our solar system and speculate about what unique processes on Earth have given rise to this unusual crustal distribution.

Review of Particle Physics

Abstract: The Review summarizes much of particle physics and cosmology. Using data from previous editions, plus 3,283 new measurements from 899 Japers, we list, evaluate, and average measured properties of gauge bosons and the recently discovered Higgs boson, leptons, quarks, mesons, and baryons. We summarize searches for hypothetical particles such as heavy neutrinos, supersymmetric and technicolor particles, axions, dark photons, etc. 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 Supersymmetry, Extra Dimensions, Particle Detectors, Probability, and Statistics. Among the 112 reviews are many that are new or heavily revised including those on: Dark Energy, Higgs Boson Physics, Electroweak Model, Neutrino Cross Section Measurements, Monte Carlo Neutrino Generators, Top Quark, Dark Matter, Dynamical Electroweak Symmetry Breaking, Accelerator Physics of Colliders, High-Energy Collider Parameters, Big Bang Nucleosynthesis, Astrophysical Constants and Cosmological Parameters.

Kraken: ultrafast metagenomic sequence classification using exact alignments

Abstract: Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences. Previous programs designed for this task have been relatively slow and computationally expensive, forcing researchers to use faster abundance estimation programs, which only classify small subsets of metagenomic data. Using exact alignment of k-mers, Kraken achieves classification accuracy comparable to the fastest BLAST program. In its fastest mode, Kraken classifies 100 base pair reads at a rate of over 4.1 million reads per minute, 909 times faster than Megablast and 11 times faster than the abundance estimation program MetaPhlAn. Kraken is available at http://ccb.jhu.edu/software/kraken/.

Root mean square error (RMSE) or mean absolute error (MAE)? – Arguments against avoiding RMSE in the literature

Abstract: . Both the root mean square error (RMSE) and the mean absolute error (MAE) are regularly employed in model evaluation studies. Willmott and Matsuura (2005) have suggested that the RMSE is not a good indicator of average model performance and might be a misleading indicator of average error, and thus the MAE would be a better metric for that purpose. While some concerns over using RMSE raised by Willmott and Matsuura (2005) and Willmott et al. (2009) are valid, the proposed avoidance of RMSE in favor of MAE is not the solution. Citing the aforementioned papers, many researchers chose MAE over RMSE to present their model evaluation statistics when presenting or adding the RMSE measures could be more beneficial. In this technical note, we demonstrate that the RMSE is not ambiguous in its meaning, contrary to what was claimed by Willmott et al. (2009). The RMSE is more appropriate to represent model performance than the MAE when the error distribution is expected to be Gaussian. In addition, we show that the RMSE satisfies the triangle inequality requirement for a distance metric, whereas Willmott et al. (2009) indicated that the sums-of-squares-based statistics do not satisfy this rule. In the end, we discussed some circumstances where using the RMSE will be more beneficial. However, we do not contend that the RMSE is superior over the MAE. Instead, a combination of metrics, including but certainly not limited to RMSEs and MAEs, are often required to assess model performance.

Minfi: A flexible and comprehensive Bioconductor package for the analysis of Infinium DNA Methylation microarrays

Abstract: Motivation The recently released Infinium HumanMethylation450 array (the '450k' array) provides a high-throughput assay to quantify DNA methylation (DNAm) at ∼450 000 loci across a range of genomic features. Although less comprehensive than high-throughput sequencing-based techniques, this product is more cost-effective and promises to be the most widely used DNAm high-throughput measurement technology over the next several years. Results Here we describe a suite of computational tools that incorporate state-of-the-art statistical techniques for the analysis of DNAm data. The software is structured to easily adapt to future versions of the technology. We include methods for preprocessing, quality assessment and detection of differentially methylated regions from the kilobase to the megabase scale. We show how our software provides a powerful and flexible development platform for future methods. We also illustrate how our methods empower the technology to make discoveries previously thought to be possible only with sequencing-based methods. Availability and implementation http://bioconductor.org/packages/release/bioc/html/minfi.html. Contact khansen@jhsph.edu; rafa@jimmy.harvard.edu Supplementary information Supplementary data are available at Bioinformatics online.

Transiting Exoplanet Survey Satellite

Abstract: The Transiting Exoplanet Survey Satellite (TESS) will search for planets transiting bright and nearby stars. TESS has been selected by NASA for launch in 2017 as an Astrophysics Explorer mission. The spacecraft will be placed into a highly elliptical 13.7-day orbit around the Earth. During its 2-year mission, TESS will employ four wide-field optical charge-coupled device cameras to monitor at least 200,000 main-sequence dwarf stars with I C ≈4−13 for temporary drops in brightness caused by planetary transits. Each star will be observed for an interval ranging from 1 month to 1 year, depending mainly on the star’s ecliptic latitude. The longest observing intervals will be for stars near the ecliptic poles, which are the optimal locations for follow-up observations with the James Webb Space Telescope. Brightness measurements of preselected target stars will be recorded every 2 min, and full frame images will be recorded every 30 min. TESS stars will be 10 to 100 times brighter than those surveyed by the pioneering Kepler mission. This will make TESS planets easier to characterize with follow-up observations. TESS is expected to find more than a thousand planets smaller than Neptune, including dozens that are comparable in size to the Earth. Public data releases will occur every 4 months, inviting immediate community-wide efforts to study the new planets. The TESS legacy will be a catalog of the nearest and brightest stars hosting transiting planets, which will endure as highly favorable targets for detailed investigations.

The biodiversity of species and their rates of extinction, distribution, and protection

Abstract: Background A principal function of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) is to “perform regular and timely assessments of knowledge on biodiversity.” In December 2013, its second plenary session approved a program to begin a global assessment in 2015. The Convention on Biological Diversity (CBD) and five other biodiversity-related conventions have adopted IPBES as their science-policy interface, so these assessments will be important in evaluating progress toward the CBD’s Aichi Targets of the Strategic Plan for Biodiversity 2011–2020. As a contribution toward such assessment, we review the biodiversity of eukaryote species and their extinction rates, distributions, and protection. We document what we know, how it likely differs from what we do not, and how these differences affect biodiversity statistics. Interestingly, several targets explicitly mention “known species”—a strong, if implicit, statement of incomplete knowledge. We start by asking how many species are known and how many remain undescribed. We then consider by how much human actions inflate extinction rates. Much depends on where species are, because different biomes contain different numbers of species of different susceptibilities. Biomes also suffer different levels of damage and have unequal levels of protection. How extinction rates will change depends on how and where threats expand and whether greater protection counters them. Different visualizations of species biodiversity. ( A ) The distributions of 9927 bird species. ( B ) The 4964 species with smaller than the median geographical range size. ( C ) The 1308 species assessed as threatened with a high risk of extinction by BirdLife International for the Red List of Threatened Species of the International Union for Conservation of Nature. ( D ) The 1080 threatened species with less than the median range size. (D) provides a strong geographical focus on where local conservation actions can have the greatest global impact. Additional biodiversity maps are available at www.biodiversitymapping.org. Advances Recent studies have clarified where the most vulnerable species live, where and how humanity changes the planet, and how this drives extinctions. These data are increasingly accessible, bringing greater transparency to science and governance. Taxonomic catalogs of plants, terrestrial vertebrates, freshwater fish, and some marine taxa are sufficient to assess their status and the limitations of our knowledge. Most species are undescribed, however. The species we know best have large geographical ranges and are often common within them. Most known species have small ranges, however, and such species are typically newer discoveries. The numbers of known species with very small ranges are increasing quickly, even in well-known taxa. They are geographically concentrated and are disproportionately likely to be threatened or already extinct. We expect unknown species to share these characteristics. Current rates of extinction are about 1000 times the background rate of extinction. These are higher than previously estimated and likely still underestimated. Future rates will depend on many factors and are poised to increase. Finally, although there has been rapid progress in developing protected areas, such efforts are not ecologically representative, nor do they optimally protect biodiversity. Outlook Progress on assessing biodiversity will emerge from continued expansion of the many recently created online databases, combining them with new global data sources on changing land and ocean use and with increasingly crowdsourced data on species’ distributions. Examples of practical conservation that follow from using combined data in Colombia and Brazil can be found at www.savingspecies.org and www.youtube.com/watch?v=R3zjeJW2NVk.

First results from the LUX dark matter experiment at the Sanford Underground Research Facility

Abstract: The Large Underground Xenon (LUX) experiment is a dual-phase xenon time-projection chamber operating at the Sanford Underground Research Facility (Lead, South Dakota). The LUX cryostat was filled for the first time in the underground laboratory in February 2013. We report results of the first WIMP search data set, taken during the period from April to August 2013, presenting the analysis of 85.3 live days of data with a fiducial volume of 118 kg. A profile-likelihood analysis technique shows our data to be consistent with the background-only hypothesis, allowing 90% confidence limits to be set on spin-independent WIMP-nucleon elastic scattering with a minimum upper limit on the cross section of 7.6 × 10(-46) cm(2) at a WIMP mass of 33 GeV/c(2). We find that the LUX data are in disagreement with low-mass WIMP signal interpretations of the results from several recent direct detection experiments.

CHARMM-GUI Membrane Builder Toward Realistic Biological Membrane Simulations

Abstract: CHARMM-GUI Membrane Builder, http://www.charmm-gui.org/input/membrane, is a web-based user interface designed to interactively build all-atom protein/membrane or membrane-only systems for molecular dynamics simulations through an automated optimized process. In this work, we describe the new features and major improvements in Membrane Builder that allow users to robustly build realistic biological membrane systems, including (1) addition of new lipid types, such as phosphoinositides, cardiolipin (CL), sphingolipids, bacterial lipids, and ergosterol, yielding more than 180 lipid types, (2) enhanced building procedure for lipid packing around protein, (3) reliable algorithm to detect lipid tail penetration to ring structures and protein surface, (4) distance-based algorithm for faster initial ion displacement, (5) CHARMM inputs for P21 image transformation, and (6) NAMD equilibration and production inputs. The robustness of these new features is illustrated by building and simulating a membrane model of the polar and septal regions of E. coli membrane, which contains five lipid types: CL lipids with two types of acyl chains and phosphatidylethanolamine lipids with three types of acyl chains. It is our hope that CHARMM-GUI Membrane Builder becomes a useful tool for simulation studies to better understand the structure and dynamics of proteins and lipids in realistic biological membrane environments. © 2014 Wiley Periodicals, Inc.

Human Action Recognition by Representing 3D Skeletons as Points in a Lie Group

Abstract: Recently introduced cost-effective depth sensors coupled with the real-time skeleton estimation algorithm of Shotton et al. [16] have generated a renewed interest in skeleton-based human action recognition. Most of the existing skeleton-based approaches use either the joint locations or the joint angles to represent a human skeleton. In this paper, we propose a new skeletal representation that explicitly models the 3D geometric relationships between various body parts using rotations and translations in 3D space. Since 3D rigid body motions are members of the special Euclidean group SE(3), the proposed skeletal representation lies in the Lie group SE(3)×…×SE(3), which is a curved manifold. Using the proposed representation, human actions can be modeled as curves in this Lie group. Since classification of curves in this Lie group is not an easy task, we map the action curves from the Lie group to its Lie algebra, which is a vector space. We then perform classification using a combination of dynamic time warping, Fourier temporal pyramid representation and linear SVM. Experimental results on three action datasets show that the proposed representation performs better than many existing skeletal representations. The proposed approach also outperforms various state-of-the-art skeleton-based human action recognition approaches.

Expanded graphite as superior anode for sodium-ion batteries

Abstract: Graphite, as the most common anode for commercial Li-ion batteries, has been reported to have a very low capacity when used as a Na-ion battery anode. It is well known that electrochemical insertion of Na(+) into graphite is significantly hindered by the insufficient interlayer spacing. Here we report expanded graphite as a Na-ion battery anode. Prepared through a process of oxidation and partial reduction on graphite, expanded graphite has an enlarged interlayer lattice distance of 4.3 A yet retains an analogous long-range-ordered layered structure to graphite. In situ transmission electron microscopy has demonstrated that the Na-ion can be reversibly inserted into and extracted from expanded graphite. Galvanostatic studies show that expanded graphite can deliver a high reversible capacity of 284 mAh g(-1) at a current density of 20 mA g(-1), maintain a capacity of 184 mAh g(-1) at 100 mA g(-1), and retain 73.92% of its capacity after 2,000 cycles.

Methane storage in metal–organic frameworks

Abstract: Natural gas (NG), whose main component is methane, is an attractive fuel for vehicular applications. Realization of safe, cheap and convenient means and materials for high-capacity methane storage can significantly facilitate the implementation of natural gas fuelled vehicles. The physisorption based process involving porous materials offers an efficient storage methodology and the emerging porous metal-organic frameworks have been explored as potential candidates because of their extraordinarily high porosities, tunable pore/cage sizes and easily immobilized functional sites. In this view, we provide an overview of the current status of metal-organic frameworks for methane storage.

Observation of high-energy astrophysical neutrinos in three years of icecube data

Abstract: A search for high-energy neutrinos interacting within the IceCube detector between 2010 and 2012 provided the first evidence for a high-energy neutrino flux of extraterrestrial origin. Results from an analysis using the same methods with a third year (2012-2013) of data from the complete IceCube detector are consistent with the previously reported astrophysical flux in the 100 TeV-PeV range at the level of 10(-8) GeV cm(-2) s(-1) sr(-1) per flavor and reject a purely atmospheric explanation for the combined three-year data at 5.7 sigma. The data are consistent with expectations for equal fluxes of all three neutrino flavors and with isotropic arrival directions, suggesting either numerous or spatially extended sources. The three-year data set, with a live time of 988 days, contains a total of 37 neutrino candidate events with deposited energies ranging from 30 to 2000 TeV. The 2000-TeV event is the highest-energy neutrino interaction ever observed.

Clouds in the atmosphere of the super-Earth exoplanet GJ 1214b

Abstract: Recent surveys have revealed that planets intermediate in size between Earth and Neptune (‘super-Earths’) are among the most common planets in the Galaxy. Atmospheric studies are the next step towards developing a comprehensive understanding of this new class of object. Much effort has been focused on using transmission spectroscopy to characterize the atmosphere of the super-Earth archetype GJ 1214b, but previous observations did not have sufficient precision to distinguish between two interpretations for the atmosphere. The planet’s atmosphere could be dominated by relatively heavy molecules, such as water (for example, a 100 per cent water vapour composition), or it could contain high-altitude clouds that obscure its lower layers. Here we report a measurement of the transmission spectrum of GJ 1214b at near-infrared wavelengths that definitively resolves this ambiguity. The data, obtained with the Hubble Space Telescope, are sufficiently precise to detect absorption features from a high mean-molecular-mass atmosphere. The observed spectrum, however, is featureless. We rule out cloud-free atmospheric models with compositions dominated by water, methane, carbon monoxide, nitrogen or carbon dioxide at greater than 5σ confidence. The planet’s atmosphere must contain clouds to be consistent with the data.

Convolutional Neural Networks for No-Reference Image Quality Assessment

Abstract: In this work we describe a Convolutional Neural Network (CNN) to accurately predict image quality without a reference image. Taking image patches as input, the CNN works in the spatial domain without using hand-crafted features that are employed by most previous methods. The network consists of one convolutional layer with max and min pooling, two fully connected layers and an output node. Within the network structure, feature learning and regression are integrated into one optimization process, which leads to a more effective model for estimating image quality. This approach achieves state of the art performance on the LIVE dataset and shows excellent generalization ability in cross dataset experiments. Further experiments on images with local distortions demonstrate the local quality estimation ability of our CNN, which is rarely reported in previous literature.

Graphene Oxide Membranes for Ionic and Molecular Sieving

Abstract: Ionic and molecular sieving membranes that enable fast solute separations from aqueous solutions are essential for processes such as water purification and desalination, sensing, and energy production ( 1 – 3 ). The two-dimensional structure and tunable physicochemical properties of graphene oxide (GO) offer an exciting opportunity to make a fundamentally new class of sieving membranes by stacking GO nanosheets ( 4 – 6 ). In the layered GO membrane, water molecules permeate through the interconnected nanochannels formed between GO nanosheets and follow a tortuous path primarily over the hydrophobic nonoxidized surface rather than the hydrophilic oxidized region of GO ( 7 ). The nearly frictionless surface of the non-oxidized GO facilitates the extremely fast flow of water molecules ( 5 ). On page 752 of this issue, Joshi et al. ( 8 ) further report that ions smaller in size than the GO nanochannel can permeate in the GO membrane at a speed orders of magnitude faster than would occur through simple diffusion. Size exclusion appears to be the dominant sieving mechanism.

Finite Elements and Fast Iterative Solvers: with Applications in Incompressible Fluid Dynamics

Abstract: The intended readership includes graduate students and researchers in engineering, numerical analysis, applied mathematics and interdisciplinary scientific computing. The publisher describes the book as follows: * An excellent introduction to finite elements, iterative linear solvers and scientific computing * Contains theoretical problems and practical exercises * All methods and examples use freely available software * Focuses on theory and computation, not theory for computation * Describes approximation methods and numerical linear algebra

Massive molecular outflows and evidence for AGN feedback from CO observations

Abstract: We study the properties of massive, galactic-scale outflows of molecular gas and investigate their impact on galaxy evolution. We present new IRAMPdBI CO(1-0) observations of local ultra-luminous infrared galaxies (ULIRGs) and quasar-hosts: a clear signature of massive and energetic molecular outflows, extending on kpc scales, is found in the CO(1-0) kinematics of four out of seven sources, with measured outflow rates of several 100M(circle dot)yr(-1). We combine these new observations with data from the literature, and explore the nature and origin of massive molecular outflows within an extended sample of 19 local galaxies. We find that starburst-dominated galaxies have an outflow rate comparable to their star formation rate (SFR), or even higher by a factor of similar to 2-4, implying that starbursts can indeed be effective in removing cold gas from galaxies. Nevertheless, our results suggest that the presence of an active galactic nucleus (AGN) can boost the outflow rate by a large factor, which is found to increase with the L-AGN/L-bol ratio. The gas depletion time scales due to molecular outflows are anti-correlated with the presence and luminosity of an AGN in these galaxies, and range from a few hundred million years in starburst galaxies down to just a few million years in galaxies hosting powerful AGNs. In quasar hosts, the depletion time scales due to the outflow are much shorter than the depletion time scales due to star formation. We estimate the outflow kinetic power and find that, for galaxies hosting powerful AGNs, it corresponds to about 5% of the AGN luminosity, as expected by models of AGN feedback. Moreover, we find that momentum rates of about 20 L-AGN/c are common among the AGN-dominated sources in our sample. For "pure" starburst galaxies, our data tentatively support models in which outflows are mostly momentum-driven by the radiation pressure from young stars onto dusty clouds. Overall, our results indicate that, although starbursts are effective in powering massive molecular outflows, the presence of an AGN may strongly enhance such outflows, and therefore have a profound feedback effect on the evolution of galaxies by efficiently removing fuel for star formation, hence quenching star formation.

Slowing Amazon deforestation through public policy and interventions in beef and soy supply chains

Abstract: The recent 70% decline in deforestation in the Brazilian Amazon suggests that it is possible to manage the advance of a vast agricultural frontier Enforcement of laws, interventions in soy and beef supply chains, restrictions on access to credit, and expansion of protected areas appear to have contributed to this decline, as did a decline in the demand for new deforestation The supply chain interventions that fed into this deceleration are precariously dependent on corporate risk management, and public policies have relied excessively on punitive measures Systems for delivering positive incentives for farmers to forgo deforestation have been designed but not fully implemented Territorial approaches to deforestation have been effective and could consolidate progress in slowing deforestation while providing a framework for addressing other important dimensions of sustainable development

Detection of an unidentified emission line in the stacked X-ray spectrum of galaxy clusters

Abstract: We detect a weak unidentified emission line at E = (3.55-3.57) ± 0.03 keV in a stacked XMM-Newton spectrum of 73 galaxy clusters spanning a redshift range 0.01-0.35. When the full sample is divided into three subsamples (Perseus, Centaurus+Ophiuchus+Coma, and all others), the line is seen at >3σ statistical significance in all three independent MOS spectra and the PN "all others" spectrum. It is also detected in the Chandra spectra of the Perseus Cluster. However, it is very weak and located within 50-110 eV of several known lines. The detection is at the limit of the current instrument capabilities. We argue that there should be no atomic transitions in thermal plasma at this energy. An intriguing possibility is the decay of sterile neutrino, a long-sought dark matter particle candidate. Assuming that all dark matter is in sterile neutrinos with ms = 2E = 7.1 keV, our detection corresponds to a neutrino decay rate consistent with previous upper limits. However, based on the cluster masses and distances, the line in Perseus is much brighter than expected in this model, significantly deviating from other subsamples. This appears to be because of an anomalously bright line at E = 3.62 keV in Perseus, which could be an Ar XVII dielectronic recombination line, although its emissivity would have to be 30 times the expected value and physically difficult to understand. Another alternative is the above anomaly in the Ar line combined with the nearby 3.51 keV K line also exceeding expectation by a factor of 10-20. Confirmation with Astro-H will be critical to determine the nature of this new line.

Transiting Exoplanet Survey Satellite (TESS)

Abstract: The Transiting Exoplanet Survey Satellite (TESS) will discover thousands of exoplanets in orbit around the brightest stars in the sky. In a two-year survey, TESS will monitor more than 500,000 stars for temporary drops in brightness caused by planetary transits. This first-ever spaceborne all-sky transit survey will identify planets ranging from Earth-sized to gas giants, around a wide range of stellar types and orbital distances. No ground-based survey can achieve this feat. A large fraction of TESS target stars will be 30-100 times brighter than those observed by Kepler satellite, and therefore TESS . planets will be far easier to characterize with follow-up observations. TESS will make it possible to study the masses, sizes, densities, orbits, and atmospheres of a large cohort of small planets, including a sample of rocky worlds in the habitable zones of their host stars. TESS will provide prime targets for observation with the James Webb Space Telescope (JWST), as well as other large ground-based and space-based telescopes of the future. TESS data will be released with minimal delay (no proprietary period), inviting immediate community-wide efforts to study the new planets. The TESS legacy will be a catalog of the very nearest and brightest main-sequence stars hosting transiting exoplanets, thus providing future observers with the most favorable targets for detailed investigations.

The genomic substrate for adaptive radiation in African cichlid fish

Abstract: Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.

Primary forest cover loss in Indonesia over 2000–2012

Abstract: Extensive clearing of Indonesian primary forests results in increased greenhouse gas emissions and biodiversity loss However, there is no consensus on the areal extent and temporal trends of primary forest clearing in Indonesia Here we report a spatially and temporally explicit quantification of Indonesian primary forest loss, which totalled over 602 Mha from 2000 to 2012 and increased on average by 47,600 ha per year By 2012, annual primary forest loss in Indonesia was estimated to be higher than in Brazil (084 Mha and 046 Mha, respectively) Proportional loss of primary forests in wetland landforms increased and almost all clearing of primary forests occurred within degraded types, meaning logging preceded conversion processes Loss within official forest land uses that restrict or prohibit clearing totalled 40% of all loss within national forest land The increasing loss of Indonesian primary forests has significant implications for climate change mitigation and biodiversity conservation efforts Deforestation affects climate, biodiversity and other ecosystem services This study quantifies Indonesia’s increasing rate of primary forest loss, which runs counter to the declining rates of loss in Brazil The results highlight the value of thematically consistent and spatially and temporally explicit information in tracking forest change

Precision Measurement of the Proton Flux in Primary Cosmic Rays from Rigidity 1 GV to 1.8 TV with the Alpha Magnetic Spectrometer on the International Space Station

Abstract: A precise measurement of the proton flux in primary cosmic rays with rigidity (momentum/charge) from 1 GV to 1.8 TV is presented based on 300 million events. Knowledge of the rigidity dependence of the proton flux is important in understanding the origin, acceleration, and propagation of cosmic rays. We present the detailed variation with rigidity of the flux spectral index for the first time. The spectral index progressively hardens at high rigidities.

Fast Alternating Direction Optimization Methods

Abstract: Alternating direction methods are a common tool for general mathematical programming and optimization. These methods have become particularly important in the field of variational image processing, which frequently requires the minimization of nondifferentiable objectives. This paper considers accelerated (i.e., fast) variants of two common alternating direction methods: the alternating direction method of multipliers (ADMM) and the alternating minimization algorithm (AMA). The proposed acceleration is of the form first proposed by Nesterov for gradient descent methods. In the case that the objective function is strongly convex, global convergence bounds are provided for both classical and accelerated variants of the methods. Numerical examples are presented to demonstrate the superior performance of the fast methods for a wide variety of problems.

Cultivating Social Resources on Social Network Sites: Facebook Relationship Maintenance Behaviors and Their Role in Social Capital Processes

Abstract: This study explores the relationship between perceived bridging social capital and specific Facebook-enabled communication behaviors using survey data from a sample of U.S. adults N=614. We explore the role of a specific set of Facebook behaviors that support relationship maintenance and assess the extent to which demographic variables, time on site, total and "actual" Facebook Friends, and this new measure Facebook Relationship Maintenance Behaviors predict bridging social capital. Drawing upon scholarship on social capital and relationship maintenance, we discuss the role of social grooming and attention-signaling activities in shaping perceived access to resources in one's network as measured by bridging social capital.

Longitudinal analysis of microbial interaction between humans and the indoor environment.

Abstract: The bacteria that colonize humans and our built environments have the potential to influence our health. Microbial communities associated with seven families and their homes over 6 weeks were assessed, including three families that moved their home. Microbial communities differed substantially among homes, and the home microbiome was largely sourced from humans. The microbiota in each home were identifiable by family. Network analysis identified humans as the primary bacterial vector, and a Bayesian method significantly matched individuals to their dwellings. Draft genomes of potential human pathogens observed on a kitchen counter could be matched to the hands of occupants. After a house move, the microbial community in the new house rapidly converged on the microbial community of the occupants' former house, suggesting rapid colonization by the family's microbiota.

The genomic substrate for adaptive radiation in African cichlid fish

Abstract: Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.