Miracle-dz/UniFAR-FTUs huggingface dataset:
Ecomorph or Endangered Coral? DNA and Microstructure Reveal Hawaiian Species Complexes: Montipora dilatata/flabellata/turgescens & M. patula/verrilli

M. dilatata, M. flabellata, and M. patula and 80 other scleractinian corals were petitioned to be listed under the US Endangered Species Act (ESA), which would have major conservation implications. One of the difficulties with this evaluation is that reproductive boundaries between morphologically defined coral species are often permeable, and morphology can be wildly variable. We examined genetic and morphological variation in Hawaiian Montipora with a suite of molecular markers (mitochondrial: COI, CR, Cyt-B, 16S, ATP6; nuclear: ATPsβ, ITS) and microscopic skeletal measurements. Mitochondrial markers and the ITS region revealed four distinct clades: I) M. patula/M. verrilli, II) M. cf. incrassata, III) M. capitata, IV) M. dilatata/M. flabellata/M. cf. turgescens. These clades are likely to occur outside of Hawai'i according to mitochondrial control region haplotypes from previous studies. The ATPsβ intron data showed a pattern often interpreted as resulting from hybridization and introgression; however, incomplete lineage sorting may be more likely since the multicopy nuclear ITS region was consistent with the mitochondrial data. Furthermore, principal components analysis (PCA) of skeletal microstructure was concordant with the mitochondrial clades, while nominal taxa overlapped. The size and shape of verrucae or papillae contributed most to identifying groups, while colony-level morphology was highly variable. It is not yet clear if these species complexes represent population-level variation or incipient speciation (CA<1MYA), two alternatives that have very different conservation implications. This study highlights the difficulty in understanding the scale of genetic and morphological variation that corresponds to species as opposed to population-level variation, information that is essential for conservation and for understanding coral biodiversity.
Distinguishing Attributes for the Operationally Responsive Space Paradigm

The value-centric perspective of operationally responsive space (ORS) places emphasis on meeting the needs of stakeholders in a timely and effective manner. While ongoing technology developments for spacecraft standardization and rapid launch as well as efforts to develop enabling concepts of operations, tactics, and procedures support the advancement of an ORS paradigm, little work has been completed to evaluate responsive architectures using value-based design methods. To address this gap, Multi-Attribute Tradespace Exploration (MATE), a conceptual design methodology that applies decision theory to model and simulation-based design, is applied to the assessment of ORS and “big space” approaches for a notional intelligence, surveillance, and reconnaissance mission. Decoupling the design from the need through tradespace exploration, MATE is both a solution-generating as well as a decision-making framework. The focus in this paper is on the front-end of the MATE process—eliciting preferences from system stakeholders, including decision makers that have significant influence over the allocation of resources in a development effort. These preferences are captured in a multiattribute utility function for guiding subsequent tradespace exploration. After enumerating both traditional and responsive attributes for a notional intelligence, surveillance, and reconnaissance mission, the implications of the expanded set of attributes for the MATE modeling architecture are discussed. A model for incorporating schedule as an independent variable within tradespace studies is proposed, as is future work on the identification of mission areas and operational contexts suitable to the ORS paradigm. Overall, the key contribution of the paper is setting up the application of a value-centric methodology for the objective assessment of operationally responsive architectures.
Multipath Wireless Network Coding: An Augmented Potential Game Perspective

We consider wireless networks in which multiple paths are available between each source and destination. We allow each source to split traffic among all of its available paths, and we ask the question: How do we attain the lowest possible number of transmissions per unit time to support a given traffic matrix? Traffic bound in opposite directions over two wireless hops can utilize the “reverse carpooling” advantage of network coding in order to decrease the number of transmissions used. We call such coded hops “hyper-links. ” With the reverse carpooling technique, longer paths might be cheaper than shorter ones. However, there is a peculiar situation among sources-the network coding advantage is realized only if there is traffic in both directions of a shared path. We consider the problem of routing with network coding by selfish agents (the sources) as a potential game and develop a method of state-space augmentation in which additional agents (the hyper-links) decouple sources' choices from each other by declaring a hyper-link capacity, allowing sources to split their traffic selfishly in a distributed fashion, and then changing the hyper-link capacity based on user actions. Furthermore, each hyper-link has a scheduling constraint in terms of the maximum number of transmissions allowed per unit time. We show that our two-level control scheme is stable and verify our analytical insights by simulation.
Sphingoid Bases Inhibit Acid-Induced Demineralization of Hydroxyapatite

Calcium hydroxyapatite (HAp), the main constituent of dental enamel, is inherently susceptible to the etching and dissolving action of acids, resulting in tooth decay such as dental caries and dental erosion. Since the prevalence of erosive wear is gradually increasing, there is urgent need for agents that protect the enamel against erosive attacks. In the present study we studied in vitro the anti-erosive effects of a number of sphingolipids and sphingoid bases, which form the backbone of sphingolipids. Pretreatment of HAp discs with sphingosine, phytosphingosine (PHS), PHS phosphate and sphinganine significantly protected these against acid-induced demineralization by 80 ± 17%, 78 ± 17%, 78 ± 7% and 81 ± 8%, respectively (p < 0.001). On the other hand, sphingomyelin, acetyl PHS, octanoyl PHS and stearoyl PHS had no anti-erosive effects. Atomic force measurement revealed that HAp discs treated with PHS were almost completely and homogeneously covered by patches of PHS. This suggests that PHS and other sphingoid bases form layers on the surface of HAp, which act as diffusion barriers against H+ ions. In principle, these anti-erosive properties make PHS and related sphingosines promising and attractive candidates as ingredients in oral care products. © 2014 S. Karger AG, Basel
Effects of four distances on communication processes in global software projects

Global distribution of software engineering introduces geographical, temporal, cultural and organizational distance into teamwork. Globally distributed software projects need to use electronic communication tools to collaborate across these distances. Communication media differ in properties and capabilities to overcome the challenges imposed by these distances. In this paper, we examine the effects of these four distances to communication in software engineering projects. We use Media Synchronicity Theory as a framework to analyze the capabilities of different communication media to support software engineering across distances. We report our findings on the relationship between communication media and distance from three distributed software projects. Based on the results, we aim at providing conclusions on choosing communication media for globally distributed software projects.
Using Nonmetric Multidimensional Scaling to Analyze Bee Visitation in East Tennessee Crops as an Indicator of Pollination Services Provided by Honey Bees (Apis mellifera L.) and Native Bees

Abstract This study investigated bee visitation on 10 agricultural crops grown on diverse small farms in Tennessee to determine the abundance of native bees and honey bees and the partitioning of visitation among crops. Summaries for each crop are used to generate mean proportions of bee visitation by categories of bees. This shows that native bee visits often occur as frequently, or in greater proportions than non-native honey bee visits. Visitation across multiple crops is then analyzed together with nonmetric multidimensional scaling to show how communities of bees that provide crop pollination change depending on the crop. Within squash and pumpkin plantings, continuous and discrete factors, such as “time of day” and “organic practices,” further explain shifts in the community composition of flower visitors. Results from this study show that native bees frequently visit flowers on various crops, indicating that they are likely contributing to pollination services in addition to honey bees. Furthermore, the community of bees visiting flowers changes based on crop type, phenology, and spatial-temporal factors. Results suggest that developing pollinator conservation for farms that grow a wide variety of crops will likely require multiple conservation strategies. Farms that concentrate on a single crop may be able to tailor conservation practices toward the most important bees in their system and geographic locale.
ROSETTA for Single Trace Analysis Recovery Of Secret Exponent by Triangular Trace Analysis

In most ecient exponentiation implementations, recovering the secret exponent is equivalent to disclosing the sequence of squaring and multiplication operations. Some known attacks on the RSA exponen- tiation apply this strategy, but cannot be used against classical blinding countermeasures. In this paper, we propose new attacks distinguishing squaring from multiplications using a single side-channel trace. It makes our attacks more robust against blinding countermeasures than previous methods even if both exponent and message are randomized, whatever the quality and length of random masks. We demonstrate the eciency of our new techniques using simulations in dierent noise congurations.
Earliest Holocene deglaciation of the central Uummannaq Fjord system, West Greenland

Uummannaq Fjord, West Greenland, held the Uummannaq Ice Stream system that drained an estimated ~6% of the Greenland Ice Sheet (GrIS) during the Last Glacial Maximum. Published ages for the final deglaciation in Uummannaq Fjord vary from as early as c. 9.8 ka to as late as c. 5.3 ka. Assessing this variability requires additional chronological controls to improve the deglaciation history of central West Greenland. Here, we combine 14C dating of lake sediment cores with cosmogenic 10Be exposure dating at sites adjacent to the present GrIS margin in the central‐inland sector of the Uummannaq Fjord system. We find that ice retreated to or within the present GrIS margin at 10.8±0.2 ka (n = 6). Although this ‘final deglaciation’ to or within the present GrIS margin across the Uummannaq Fjord system varies from c. 10.8 to 5.3 ka, all chronologies indicate collapse from the continental shelf to the inner fjords at c. 11.0 ka, which occurred at a net retreat rate of 300–1100 m a−1. The Uummannaq Fjord system deglaciated c. 1000 years earlier than the major fjord system to the south, Disko Bugt. However, similarly rapid retreat rates of the two palaeo‐ice stream systems suggest that their collapse may have been aided by high calving rates. The asynchronous deglaciation of the GrIS throughout the Uummannaq Fjord system probably relates to the influence of varying fjord geometry on marine glacier behaviour.
ArrayBridge: Interweaving declarative array processing with high-performance computing

Author(s): Xing, Haoyuan; Floratos, Sofoklis; Blanas, Spyros; Byna, Suren; Prabhat; Wu, Kesheng; Brown, Paul | Abstract: Scientists are increasingly turning to datacenter-scale computers to produce and analyze massive arrays. Despite decades of database research that extols the virtues of declarative query processing, scientists still write, debug and parallelize imperative HPC kernels even for the most mundane queries. This impedance mismatch has been partly attributed to the cumbersome data loading process; in response, the database community has proposed in situ mechanisms to access data in scientific file formats. Scientists, however, desire more than a passive access method that reads arrays from files. This paper describes ArrayBridge, a bi-directional array view mechanism for scientific file formats, that aims to make declarative array manipulations interoperable with imperative file-centric analyses. Our prototype implementation of ArrayBridge uses HDF5 as the underlying array storage library and seamlessly integrates into the SciDB open-source array database system. In addition to fast querying over external array objects, ArrayBridge produces arrays in the HDF5 file format just as easily as it can read from it. ArrayBridge also supports time travel queries from imperative kernels through the unmodified HDF5 API, and automatically deduplicates between array versions for space efficiency. Our extensive performance evaluation in NERSC, a large-scale scientific computing facility, shows that ArrayBridge exhibits statistically indistinguishable performance and I/O scalability to the native SciDB storage engine.
Multi‐locus DNA sequence data reveal a history of deep cryptic vicariance and habitat‐driven convergence in the desert night lizard Xantusia vigilis species complex (Squamata: Xantusiidae)

The lizard genus Xantusia of southwestern North America has received recent attention in relation to delimiting species. Using more than 500 lizards from 156 localities, we further test hypothesized species boundaries and clarify phylogeographical patterns, particularly in regions of potential secondary contact. We sequenced the entire mitochondrial cytochrome b gene for every lizard in the study, plus a second mitochondrial DNA (mtDNA) region and two nuclear introns for subsets of the total sample. Phylogenetic analyses of the mtDNA recover a well‐resolved, novel hypothesis for species in the Xantusia vigilis complex. The nuclear DNA (nDNA) data provide independent support for the recognition of X. arizonae, X. bezyi and X. wigginsi. Differences between the respective mtDNA and nDNA topologies result from either the effects of lineage sorting or ancient introgression. Nuclear data confirm the inference that some populations of X. vigilis in northwestern Arizona converged on rock‐crevice‐dwelling morphology and are not X. arizonae with an introgressed X. vigilis mtDNA genome. The historical independence of ancient cryptic lineages of Xantusia in southern California is also corroborated, though limited introgression is detected. Our proposed biogeographical scenario indicates that diversification of this group was driven by vicariance beginning in the late Miocene. Additionally, Pleistocene climatical changes influenced Xantusia distribution, and the now inhospitable Colorado Desert previously supported night lizard presence. The current taxonomy of the group likely underestimates species diversity within the group, and our results collectively show that while convergence on the rock‐crevice‐dwelling morphology is one hallmark of Xantusia evolution, morphological stasis is paradoxically another.
Self-adaptive segmentation of satellite images based on a weighted aggregation approach

Image segmentation is a decisive process in object-based image analysis, while the uncertainty of segmentation scales can significantly influence the results. To resolve this issue, this study proposes a Self-Adaptive Segmentation (SAS) method which bridges the gap between the inherent scale and segmentation scale of each object. Firstly, SAS is defined as a variable-scale segmentation approach, aiming at generating local optimum results. It is then implemented based on Segmentation by Weighted Aggregation (SWA) method and optimized by selfhood scale estimation technique. Secondly, two images derived from WorldView-2 (an urban area) and Landsat-8 (a farmland area) are employed to verify the effectiveness and adaptability of this method. Thirdly, it is further compared with SWA and mean shift method by reference to two evaluations, including an unsupervised evaluation, i.e., Global Score (GS), and a supervised one named Geometry-based comparison. The experimental results indicate the SAS method presented in this study is effective in solving the scale issues in multiscale segmentations. It shows higher accuracy than SWA through assigning an appropriate segmentation scale for each object. Moreover, the segmentation results achieved by SAS method in both study areas are more accurate than those by mean shift method, which demonstrates the stable performance of SAS method across diverse scenes and data sets. This advantage is more obvious in farmland area than in urban scene, according to the accuracy assessment results.
Configuration of and Interaction Between Information Security Technologies: The Case of Firewalls and Intrusion Detection Systems

Proper configuration of security technologies is critical to balance the needs for access and protection of information. The common practice of using a layered security architecture that has multiple technologies amplifies the need for proper configuration because the configuration decision about one security technology has ramifications for the configuration decisions about others. Furthermore, security technologies rely on each other for their operations, thereby affecting each other's contribution. In this paper we study configuration of and interaction between a firewall and intrusion detection systems (IDS). We show that deploying a technology, whether it is the firewall or the IDS, could hurt the firm if the configuration is not optimized for the firm's environment. A more serious consequence of deploying the two technologies with suboptimal configurations is that even if the firm could benefit when each is deployed alone, the firm could be hurt by deploying both. Configuring the IDS and the firewall optimally eliminates the conflict between them, ensuring that if the firm benefits from deploying each of these technologies when deployed alone, it will always benefit from deploying both. When optimally configured, we find that these technologies complement or substitute each other. Furthermore, we find that while the optimal configuration of an IDS does not change whether it is deployed alone or together with a firewall, the optimal configuration of a firewall has a lower detection rate (i.e., allowing more access) when it is deployed with an IDS than when deployed alone. Our results highlight the complex interactions between firewall and IDS technologies when they are used together in a security architecture, and, hence, the need for proper configuration to benefit from these technologies.
Monetary Policy under Uncertainty in Micro-Founded Macroeconometric Models

We use a micro-founded macroeconometric modeling framework to investigate the design of monetary policy when the central bank faces uncertainty about the true structure of the economy. We apply Bayesian methods to estimate the parameters of the baseline specification using postwar U.S. data and then determine the policy under commitment that maximizes household welfare. We find that the performance of the optimal policy is closely matched by a simple operational rule that focuses solely on stabilizing nominal wage inflation. Furthermore, this simple wage stabilization rule is robust to uncertainty about the model parameters and to various assumptions regarding the nature and incidence of the innovations. However, the characteristics of optimal policy are very sensitive to the specification of the wage-contracting mechanism, thereby highlighting the importance of additional research regarding the structure of labor markets and wage determination.
Journal of Graph Algorithms and Applications Testing Simultaneous Planarity When the Common Graph Is 2-connected

Two planar graphs G1 and G2 sharing some vertices and edges are simultaneously planar if they have planar drawings such that a shared vertex [edge] is represented by the same point [curve] in both drawings. It is an open problem whether simultaneous planarity can be tested efficiently. We give a linear-time algorithm to test simultaneous planarity when the shared graph is 2-connected. Our algorithm extends to the case of k planar graphs where each vertex [edge] is either common to all graphs or belongs to exactly one of them, and the common subgraph is 2-connected.
Soaring and Gust Response in the Steppe Eagle

This thesis explores how onboard instrumentation can be used to study how birds interact with the atmosphere, in particular to understand their soaring strategies and gust response mechanisms. The instrumentation unit consists of integrated sensors, including a GPS, IMU (inertial measurement unit) and pressure transducer, which provide accurate, high frequency measurements of the aerodynamics and kinematics of a free flying bird. The equipment development and derivation of parameters are initially presented. The data recorded from multiple flights of a steppe eagle (Aquila nipalensis) are then used to analyse the different aspects of its soaring flight throughout the rest of the thesis. First, the occurrence and mechanism of the wing tuck manoeuvre is investigated and found to be a gust response, precipitated by a drop in aerodynamic loading. It is suggested that this reduction in loading results in a moment imbalance on the wings, and that ultimately the wings are pulled down by an internal musculoskeletal moment. The bird's slope soaring behaviour is then studied by using CFD analysis to model the local updrafts for comparison with the bird's performance. The analysis shows that the bird predominantly flew in the regions of strongest updraft along the ridge but did not attempt to maximise gravitational potential energy. This leads to gliding flight and a review of the theoretical derivation of the classic glide polar. A sensitivity analysis of the polar to different drag coeffcients highlights the need for more research into the selection of suitable values. The development of a new `soaring optimisation' chart to include the effect of wind conditions on the selection of best glide speed is presented. This is then compared with experimental glide data from the bird and used to determine the optimal drag coeffcients for the polar model. Finally, a technique is developed for automatically identifying sections of thermalling flight and for removing the wind drift component to allow us to test thermalling behaviour. This exploratory analysis highlights the complexity of the flow structure within the thermal and the distinctly unsteady circling of the bird.