Michigan Technological University

We describe the third generation of the CAP sequence assembly program. The CAP3 program includes a number of improvements and new features. The program has a capability to clip 5' and 3' low-quality regions of reads. It uses base quality values in computation of overlaps between reads, construction of multiple sequence alignments of reads, and generation of consensus sequences. The program also uses forward-reverse constraints to correct assembly errors and link contigs. Results of CAP3 on four BAC data sets are presented. The performance of CAP3 was compared with that of PHRAP on a number of BAC data sets. PHRAP often produces longer contigs than CAP3 whereas CAP3 often produces fewer errors in consensus sequences than PHRAP. It is easier to construct scaffolds with CAP3 than with PHRAP on low-pass data with forward-reverse constraints.

We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.

We have studied temperature dependences of electron transport in graphene and its bilayer and found extremely low electron-phonon scattering rates that set the fundamental limit on possible charge carrier mobilities at room temperature. Our measurements show that mobilities higher than 200 000 cm2/V s are achievable, if extrinsic disorder is eliminated. A sharp (thresholdlike) increase in resistivity observed above approximately 200 K is unexpected but can qualitatively be understood within a model of a rippled graphene sheet in which scattering occurs on intraripple flexural phonons.

In this paper we present an intermediate program representation, called the program dependence graph ( PDG ), that makes explicit both the data and control dependences for each operation in a program. Data dependences have been used to represent only the relevant data flow relationships of a program. Control dependences are introduced to analogously represent only the essential control flow relationships of a program. Control dependences are derived from the usual control flow graph. Many traditional optimizations operate more efficiently on the PDG. Since dependences in the PDG connect computationally related parts of the program, a single walk of these dependences is sufficient to perform many optimizations. The PDG allows transformations such as vectorization, that previously required special treatment of control dependence, to be performed in a manner that is uniform for both control and data dependences. Program transformations that require interaction of the two dependence types can also be easily handled with our representation. As an example, an incremental approach to modifying data dependences resulting from branch deletion or loop unrolling is introduced. The PDG supports incremental optimization, permitting transformations to be triggered by one another and applied only to affected dependences.

The field of power harvesting has experienced significant growth over the past few years due to the ever-increasing desire to produce portable and wireless electronics with extended lifespans. Current portable and wireless devices must be designed to include electrochemical batteries as the power source. The use of batteries can be troublesome due to their limited lifespan, thus necessitating their periodic replacement. In the case of wireless sensors that are to be placed in remote locations, the sensor must be easily accessible or of a disposable nature to allow the device to function over extended periods of time. Energy scavenging devices are designed to capture the ambient energy surrounding the electronics and convert it into usable electrical energy. The concept of power harvesting works towards developing self-powered devices that do not require replaceable power supplies. A number of sources of harvestable ambient energy exist, including waste heat, vibration, electromagnetic waves, wind, flowing water, and solar energy. While each of these sources of energy can be effectively used to power remote sensors, the structural and biological communities have placed an emphasis on scavenging vibrational energy with piezoelectric materials. This article will review recent literature in the field of power harvesting and present the current state of power harvesting in its drive to create completely self-powered devices. © IOP Publishing Ltd.

autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

Free-flowing rivers (FFRs) support diverse, complex and dynamic ecosystems globally, providing important societal and economic services. Infrastructure development threatens the ecosystem processes, biodiversity and services that these rivers support. Here we assess the connectivity status of 12 million kilometres of rivers globally and identify those that remain free-flowing in their entire length. Only 37 per cent of rivers longer than 1,000 kilometres remain free-flowing over their entire length and 23 per cent flow uninterrupted to the ocean. Very long FFRs are largely restricted to remote regions of the Arctic and of the Amazon and Congo basins. In densely populated areas only few very long rivers remain free-flowing, such as the Irrawaddy and Salween. Dams and reservoirs and their up- and downstream propagation of fragmentation and flow regulation are the leading contributors to the loss of river connectivity. By applying a new method to quantify riverine connectivity and map FFRs, we provide a foundation for concerted global and national strategies to maintain or restore them.

I. Colin Prentice, Wolfgang Cramer, Sandy P. Harrison, Rik Leemans, Robert A. Monserud, Allen M. Solomon, Special Paper: A Global Biome Model Based on Plant Physiology and Dominance, Soil Properties and Climate, Journal of Biogeography, Vol. 19, No. 2 (Mar., 1992), pp. 117-134

UWB technology provides an excellent means for wireless positioning due to its high resolution capability in the time domain. Its ability to resolve multipath components makes it possible to obtain accurate location estimates without the need for complex estimation algorithms. In this article, theoretical limits for TOA estimation and TOA-based location estimation for UWB systems have been considered. Due to the complexity of the optimal schemes, suboptimal but practical alternatives have been emphasized. Performance limits for hybrid TOA/SS and TDOA/SS schemes have also been considered. Although the fundamental mechanisms for localization, including AOA-, TOA-, TDOA-, and SS-based methods, apply to all radio air interface, some positioning techniques are favored by UWB-based systems using ultrawide bandwidths.

A strategy used to design high capacity (>200 mAh g−1), Li2MnO3-stabilized LiMO2 (M = Mn, Ni, Co) electrodes for lithium-ion batteries is discussed. The advantages of the Li2MnO3 component and its influence on the structural stability and electrochemical properties of these layered xLi2MnO3·(1 − x)LiMO2 electrodes are highlighted. Structural, chemical, electrochemical and thermal properties of xLi2MnO3·(1 − x)LiMO2 electrodes are considered in the context of other commercially exploited electrode systems, such as LiCoO2, LiNi0.8Co0.15Al0.05O2, Li1+xMn2−xO4 and LiFePO4.

U-net is an image segmentation technique developed primarily for image segmentation tasks. These traits provide U-net with a high utility within the medical imaging community and have resulted in extensive adoption of U-net as the primary tool for segmentation tasks in medical imaging. The success of U-net is evident in its widespread use in nearly all major image modalities, from CT scans and MRI to X-rays and microscopy. Furthermore, while U-net is largely a segmentation tool, there have been instances of the use of U-net in other applications. Given that U-net's potential is still increasing, this narrative literature review examines the numerous developments and breakthroughs in the U-net architecture and provides observations on recent trends. We also discuss the many innovations that have advanced in deep learning and discuss how these tools facilitate U-net. In addition, we review the different image modalities and application areas that have been enhanced by U-net.

Mussels attach to solid surfaces in the sea. Their adhesion must be rapid, strong, and tough, or else they will be dislodged and dashed to pieces by the next incoming wave. Given the dearth of synthetic adhesives for wet polar surfaces, much effort has been directed to characterizing and mimicking essential features of the adhesive chemistry practiced by mussels. Studies of these organisms have uncovered important adaptive strategies that help to circumvent the high dielectric and solvation properties of water that typically frustrate adhesion. In a chemical vein, the adhesive proteins of mussels are heavily decorated with Dopa, a catecholic functionality. Various synthetic polymers have been functionalized with catechols to provide diverse adhesive, sealant, coating, and anchoring properties, particularly for critical biomedical applications.

Plasma-liquid interactions represent a growing interdisciplinary area of research involving plasma science, fluid dynamics, heat and mass transfer, photolysis, multiphase chemistry and aerosol science. This review provides an assessment of the state-of-the-art of this multidisciplinary area and identifies the key research challenges. The developments in diagnostics, modeling and further extensions of cross section and reaction rate databases that are necessary to address these challenges are discussed. The review focusses on non-equilibrium plasmas.

In 2011, Lake Erie experienced the largest harmful algal bloom in its recorded history, with a peak intensity over three times greater than any previously observed bloom. Here we show that long-term trends in agricultural practices are consistent with increasing phosphorus loading to the western basin of the lake, and that these trends, coupled with meteorological conditions in spring 2011, produced record-breaking nutrient loads. An extended period of weak lake circulation then led to abnormally long residence times that incubated the bloom, and warm and quiescent conditions after bloom onset allowed algae to remain near the top of the water column and prevented flushing of nutrients from the system. We further find that all of these factors are consistent with expected future conditions. If a scientifically guided management plan to mitigate these impacts is not implemented, we can therefore expect this bloom to be a harbinger of future blooms in Lake Erie.

The consensus that humans are causing recent global warming is shared by 90%-100% of publishing climate scientists according to six independent studies by co-authors of this paper. Those results are consistent with the 97% consensus reported by Cook et al (Environ. Res. Lett. 8 024024) based on 11 944 abstracts of research papers, of which 4014 took a position on the cause of recent global warming. A survey of authors of those papers (N=2412 papers) also supported a 97% consensus. Tol (2016 Environ. Res. Lett. 11 048001) comes to a different conclusion using results from surveys of nonexperts such as economic geologists and a self-selected group of those who reject the consensus. We demonstrate that this outcome is not unexpected because the level of consensus correlates with expertise in climate science. At one point, Tol also reduces the apparent consensus by assuming that abstracts that do not explicitly state the cause of global warming ('no position') represent nonendorsement, an approach that if applied elsewhere would reject consensus on well-established theories such as plate tectonics. We examine the available studies and conclude that the finding of 97% consensus in published climate research is robust and consistent with other surveys of climate scientists and peer-reviewed studies.

Abstract: Although forest edges have been studied extensively as an important consequence of fragmentation, a unifying theory of edge influence has yet to be developed. Our objective was to take steps toward the development of such a theory by (1) synthesizing the current knowledge of patterns of forest structure and composition at anthropogenically created forest edges, (2) developing hypotheses about the magnitude and distance of edge influence that consider the ecological processes influencing these patterns, and (3) identifying needs for future research. We compiled data from 44 published studies on edge influence on forest structure and composition in boreal, temperate, and tropical forests. Abiotic and biotic gradients near created forest edges generate a set of primary responses to edge creation. Indirect effects from these primary responses and the original edge gradient perpetuate edge influence, leading to secondary responses. Further changes in vegetation affect the edge environment, resulting in ongoing edge dynamics. We suggest that the magnitude and distance of edge influence are a direct function of the contrast in structure and composition between adjacent communities on either side of the edge. Local factors such as climate, edge characteristics, stand attributes, and biotic factors affect patch contrast. Regional factors define the context within which to assess the ecological significance of edge influence (the degree to which the edge habitat differs from interior forest habitat). Our hypotheses will help predict edge influence on structure and composition in forested ecosystems, an important consideration for conservation. For future research on forest edges in fragmented landscapes, we encourage the testing of our hypotheses, the use of standardized methodology, complete descriptions of study sites, studies on other types of edges, synthesis of edge influence on different components of the ecosystem, and investigations of edges in a landscape context.

A unifying program modeling the evolution of microstructures and their effects on the macroscopic response of materials is outlined. The new physical assumption introduced is the distinction among “normal” states associated with the parent lattice and “excited” states associated with the occurring microstructures. Both states are described by the usual balance laws of continuum mechanics properly modified to account for their mechanical interaction (mass and momentum exchange). Emphasis is put on the spatial evolution of the microstructures and its nonconvex character which is stabilized by considering gradient effects. The program can lead to predictive models for the localization of microstructures and its relation to the localization of macroscopic deformation. Moreover, it provides a rigorous microstructural justification of macroscopic theories of plasticity and viscoplasticity, including isotropic and kinematic hardening, as well as various current inelastic models. Finally, it suggests a proper frame for considering large deformation and rotation effects.

Abstract We analyze the evolution of the scientific consensus on anthropogenic global warming (AGW) in the peer-reviewed scientific literature, examining 11 944 climate abstracts from 1991–2011 matching the topics ‘global climate change’ or ‘global warming’. We find that 66.4% of abstracts expressed no position on AGW, 32.6% endorsed AGW, 0.7% rejected AGW and 0.3% were uncertain about the cause of global warming. Among abstracts expressing a position on AGW, 97.1% endorsed the consensus position that humans are causing global warming. In a second phase of this study, we invited authors to rate their own papers. Compared to abstract ratings, a smaller percentage of self-rated papers expressed no position on AGW (35.5%). Among self-rated papers expressing a position on AGW, 97.2% endorsed the consensus. For both abstract ratings and authors’ self-ratings, the percentage of endorsements among papers expressing a position on AGW marginally increased over time. Our analysis indicates that the number of papers rejecting the consensus on AGW is a vanishingly small proportion of the published research.

Plants with a winter growth habit flower earlier when exposed for several weeks to cold temperatures, a process called vernalization. We report here the positional cloning of the wheat vernalization gene VRN2, a dominant repressor of flowering that is down-regulated by vernalization. Loss of function of VRN2, whether by natural mutations or deletions, resulted in spring lines, which do not require vernalization to flower. Reduction of the RNA level of VRN2 by RNA interference accelerated the flowering time of transgenic winter-wheat plants by more than a month.

Functional traits offer a rich quantitative framework for developing and testing theories in evolutionary biology, ecology and ecosystem science. However, the potential of functional traits to drive theoretical advances and refine models of global change can only be fully realised when species-level information is complete. Here we present the AVONET dataset containing comprehensive functional trait data for all birds, including six ecological variables, 11 continuous morphological traits, and information on range size and location. Raw morphological measurements are presented from 90,020 individuals of 11,009 extant bird species sampled from 181 countries. These data are also summarised as species averages in three taxonomic formats, allowing integration with a global phylogeny, geographical range maps, IUCN Red List data and the eBird citizen science database. The AVONET dataset provides the most detailed picture of continuous trait variation for any major radiation of organisms, offering a global template for testing hypotheses and exploring the evolutionary origins, structure and functioning of biodiversity.