bluuebunny/crossref_metadata_2025 huggingface dataset:
Who Will Feed China in the 21st Century? Income Growth and Food Demand and Supply in China
Authors: Fukase Emiko , Martin Will
Published: July 2015

This study uses resource‐based measures to explore the evolution of China's demand and supply for food. China's dietary shift from plant to animal‐based foods, induced by its income growth, is likely to impose considerable pressure on agricultural resources. China's demand for food on this measure appears consistent with global trends, while China is an out‐performer on the supply side, producing much more food than its income level and land endowment would predict. China's current per capita income is in a range where consumption growth is high and in excess of production growth, but the gap between supply and demand is likely to diminish as population and per capita consumption growth decelerate. Continuing agricultural productivity growth and sustainable resource management will be important influences on the growth of China's future net import demand for food.
Constructing Water Shortages on a Huge River: The Case of Shanghai
Authors: WEBBER MICHAEL , BARNET JON , CHEN ZHONGYUAN , FINLAYSON BRIAN , WANG MARK , CHEN DAN , CHEN JING , LI MAOTIAN , WEI TAOYUAN , WU SARAH , XU HAO
Published: July 2015

Shanghai is located on the world's third largest river (by volume). Yet it faces the risk of shortages of drinking water. Many decisions and environmental characteristics have contributed to this threat. First, Shanghai has become dependent on water brought into the municipality by rivers. Second, it has become increasingly reliant on water from the Changjiang (Yangzi River), principally in order to control the levels of pollution in the water that enters its treatment plants. Third, for reasons associated with inter‐provincial administrative arrangements, the city's water intakes are located within the municipality, within the estuary zone and subject to tidal intrusions of salt water. Fourth, at high tide and when the Changjiang's discharge is low, salt intrudes far into the estuary, beyond the current water intakes. If sea levels rise, these intrusions will become more pronounced. Fifth, large‐scale central government infrastructure projects (such as dams and the South‐North Transfer) are altering the hydrological characteristics of the river. Such projects raise the probability of salt water intrusions into the water intake zone. The Shanghai and central governments have thus made a series of decisions that, taken together, have led the municipality to rely on a source of drinking water that is increasingly unreliable and subject to the risk of shortages due to salt water intrusions. Why these decisions have been made – independently – is an important problem for those who would understand the provision of water for cities and the practical efficacy of Chinese governance systems.
Long‐term consequences of breastfeeding on cholesterol, obesity, systolic blood pressure and type 2 diabetes: a systematic review and meta‐analysis
Authors: Horta Bernardo L. , Loret de Mola Christian , Victora Cesar G.
Published: July 2015

Aim

To systematically review the evidence on the associations between breastfeeding and overweight/obesity, blood pressure, total cholesterol and type 2 diabetes.

Methods

Two independent literature searches were carried out using the MEDLINE, LILACS, SCIELO and Web of Science databases. Studies restricted to infants and those without an internal comparison group were excluded. Fixed‐ and random‐effects models were used to pool the estimates.

Results

Breastfed subjects were less likely to be considered obese/overweight [pooled odds ratio: 0.74 (95% confidence interval (CI): 0.70; 0.78)] (n = 113). Among the 11 high‐quality studies, the association was smaller [pooled odds ratio: 0.87 (95%CI: 0.76; 0.99)]. Total cholesterol (n = 46) was independent of breastfeeding [pooled mean difference: −0.01 mmol/L (95%CI: −0.05; 0.02)]. Systolic blood pressure (n = 43) was lower among breastfed subjects [mean difference: −0.80 (95%CI: −1.17; −0.43)], but no association was observed among larger studies, and for diastolic blood pressure (n = 38) [mean difference: −0.24 (95%CI: −0.50; 0.02)]. For type 2 diabetes (n = 11), the odds ratio was lower among those subjects who had been breastfed [pooled odds ratio: 0.65 (95%CI: 0.49; 0.86)].

Conclusion

Breastfeeding decreased the odds of type 2 diabetes and based on high‐quality studies, decreased by 13% the odds of overweight/obesity. No associations were found for total cholesterol or blood pressure.
Using Decision Lists to Construct Interpretable and Parsimonious Treatment Regimes
Authors: Zhang Yichi , Laber Eric B. , Tsiatis Anastasios , Davidian Marie
Published: July 2015

A treatment regime formalizes personalized medicine as a function from individual patient characteristics to a recommended treatment. A high-quality treatment regime can improve patient outcomes while reducing cost, resource consumption, and treatment burden. Thus, there is tremendous interest in estimating treatment regimes from observational and randomized studies. However, the development of treatment regimes for application in clinical practice requires the long-term, joint effort of statisticians and clinical scientists. In this collaborative process, the statistician must integrate clinical science into the statistical models underlying a treatment regime and the clinician must scrutinize the estimated treatment regime for scientific validity. To facilitate meaningful information exchange, it is important that estimated treatment regimes be interpretable in a subject-matter context. We propose a simple, yet flexible class of treatment regimes whose members are representable as a short list of if–then statements. Regimes in this class are immediately interpretable and are therefore an appealing choice for broad application in practice. We derive a robust estimator of the optimal regime within this class and demonstrate its finite sample performance using simulation experiments. The proposed method is illustrated with data from two clinical trials.
Merging Multiple Longitudinal Studies with Study-Specific Missing Covariates: A Joint Estimating Function Approach
Authors: Wang Fei , Song Peter X.-K. , Wang Lu
Published: July 2015

Merging multiple datasets collected from studies with identical or similar scientific objectives is often undertaken in practice to increase statistical power. This article concerns the development of an effective statistical method that enables to merge multiple longitudinal datasets subject to various heterogeneous characteristics, such as different follow-up schedules and study-specific missing covariates (e.g., covariates observed in some studies but missing in other studies). The presence of study-specific missing covariates presents great statistical methodology challenge in data merging and analysis. We propose a joint estimating function approach to addressing this challenge, in which a novel nonparametric estimating function constructed via splines-based sieve approximation is utilized to bridge estimating equations from studies with missing covariates to those with fully observed covariates. Under mild regularity conditions, we show that the proposed estimator is consistent and asymptotically normal. We evaluate finite-sample performances of the proposed method through simulation studies. In comparison to the conventional multiple imputation approach, our method exhibits smaller estimation bias. We provide an illustrative data analysis using longitudinal cohorts collected in Mexico City to assess the effect of lead exposures on children's somatic growth.
Precortical Phase of Alzheimer's Disease (AD)‐Related Tau Cytoskeletal Pathology
Authors: Stratmann Katharina , Heinsen Helmut , Korf Horst‐Werner , Del Turco Domenico , Ghebremedhin Estifanos , Seidel Kay , Bouzrou Mohamed , Grinberg Lea T. , Bohl Jürgen , Wharton Stephen B. , den Dunnen Wilfred , Rüb Udo
Published: July 2015

Alzheimer's disease (AD) represents the most frequent progressive neuropsychiatric disorder worldwide leading to dementia. We systematically investigated the presence and extent of the AD‐related cytoskeletal pathology in serial thick tissue sections through all subcortical brain nuclei that send efferent projections to the transentorhinal and entorhinal regions in three individuals with Braak and Braak AD stage 0 cortical cytoskeletal pathology and fourteen individuals with Braak and Braak AD stage I cortical cytoskeletal pathology by means of immunostainings with the anti‐tau antibody AT8. These investigations revealed consistent AT8 immunoreactive tau cytoskeletal pathology in a subset of these subcortical nuclei in the Braak and Braak AD stage 0 individuals and in all of these subcortical nuclei in the Braak and Braak AD stage I individuals. The widespread affection of the subcortical nuclei in Braak and Braak AD stage I shows that the extent of the early subcortical tau cytoskeletal pathology has been considerably underestimated previously. In addition, our novel findings support the concept that subcortical nuclei become already affected during an early ‘pre‐cortical’ evolutional phase before the first AD‐related cytoskeletal changes occur in the mediobasal temporal lobe (i.e. allocortical transentorhinal and entorhinal regions). The very early involved subcortical brain regions may represent the origin of the AD‐related tau cytoskeletal pathology, from where the neuronal cytoskeletal pathology takes an ascending course toward the secondarily affected allocortex and spreads transneuronally along anatomical pathways in predictable sequences.
Congenital adrenal hyperplasia with localized aggressive periodontitis and amelogenesis imperfecta
Authors: Ajlan Sumaiah Abdulbaqi
Published: July 2015

Congenital adrenal hyperplasia (CAH) is an inherited medical condition that implies defects in steroid biosynthesis. The dental findings of a female patient with CAH are reported. The patient suffered from severe periodontal tissue destruction, obvious enamel defects, as well as some occlusal problems. The management approach is presented and the possibility of interrelation of her dental findings with her medical condition is discussed.
Visual Analytics for the Exploration of Tumor Tissue Characterization
Authors: Raidou R.G. , van der Heide U.A. , Dinh C.V. , Ghobadi G. , Kallehauge J.F. , Breeuwer M. , Vilanova A.
Published: July 2015

Tumors are heterogeneous tissues consisting of multiple regions with distinct characteristics. Characterization of these intra‐tumor regions can improve patient diagnosis and enable a better targeted treatment. Ideally, tissue characterization could be performed non‐invasively, using medical imaging data, to derive per voxel a number of features, indicative of tissue properties. However, the high dimensionality and complexity of this imaging‐derived feature space is prohibiting for easy exploration and analysis ‐ especially when clinical researchers require to associate observations from the feature space to other reference data, e.g., features derived from histopathological data. Currently, the exploratory approach used in clinical research consists of juxtaposing these data, visually comparing them and mentally reconstructing their relationships. This is a time consuming and tedious process, from which it is difficult to obtain the required insight. We propose a visual tool for: (1) easy exploration and visual analysis of the feature space of imaging‐derived tissue characteristics and (2) knowledge discovery and hypothesis generation and confirmation, with respect to reference data used in clinical research. We employ, as central view, a 2D embedding of the imaging‐derived features. Multiple linked interactive views provide functionality for the exploration and analysis of the local structure of the feature space, enabling linking to patient anatomy and clinical reference data. We performed an initial evaluation with ten clinical researchers. All participants agreed that, unlike current practice, the proposed visual tool enables them to identify, explore and analyze heterogeneous intra‐tumor regions and particularly, to generate and confirm hypotheses, with respect to clinical reference data.
Learning Probabilistic Transfer Functions: A Comparative Study of Classifiers
Authors: Soundararajan K. P. , Schultz T.
Published: July 2015

Complex volume rendering tasks require high‐dimensional transfer functions, which are notoriously difficult to design. One solution to this is to learn transfer functions from scribbles that the user places in the volumetric domain in an intuitive and natural manner. In this paper, we explicitly model and visualize the uncertainty in the resulting classification. To this end, we extend a previous intelligent system approach to volume rendering, and we systematically compare five supervised classification techniques – Gaussian Naive Bayes, k Nearest Neighbor, Support Vector Machines, Neural Networks, and Random Forests – with respect to probabilistic classification, support for multiple materials, interactive performance, robustness to unreliable input, and easy parameter tuning, which we identify as key requirements for the successful use in this application. Based on theoretical considerations, as well as quantitative and visual results on volume datasets from different sources and modalities, we conclude that, while no single classifier can be expected to outperform all others under all circumstances, random forests are a useful off‐the‐shelf technique that provides fast, easy, robust and accurate results in many scenarios.
Rule‐Enhanced Transfer Function Generation for Medical Volume Visualization
Authors: Cai Li‐Le , Nguyen Binh P. , Chui Chee‐Kong , Ong Sim‐Heng
Published: July 2015

In volume visualization, transfer functions are used to classify the volumetric data and assign optical properties to the voxels. In general, transfer functions are generated in a transfer function space, which is the feature space constructed by data values and properties derived from the data. If volumetric objects have the same or overlapping data values, it would be difficult to separate them in the transfer function space. In this paper, we present a rule‐enhanced transfer function design method that allows important structures of the volume to be more effectively separated and highlighted. We define a set of rules based on the local frequency distribution of volume attributes. A rule‐selection method based on a genetic algorithm is proposed to learn the set of rules that can distinguish the user‐specified target tissue from other tissues. In the rendering stage, voxels satisfying these rules are rendered with higher opacities in order to highlight the target tissue. The proposed method was tested on various volumetric datasets to enhance the visualization of important structures that are difficult to be visualized by traditional transfer function design methods. The results demonstrate the effectiveness of the proposed method.
Edge‐Aware Volume Smoothing Using L0 Gradient Minimization
Authors: Wang Qichao , Tao Yubo , Lin Hai
Published: July 2015

In volume visualization, noise in regions of homogeneous material and at boundaries between different materials poses a great challenge in extracting, analyzing and rendering features of interest. In this paper, we present a novel volume denoising / smoothing method based on the L0 gradient minimization framework. This framework globally controls how many voxels with a non‐zero gradient are in the result in order to approximate important features’ structures in a sparse way. This procedure can be solved quickly by the alternating optimization strategy with half‐quadratic splitting. While the proposed L0 volume gradient minimization method can effectively remove noise in homogeneous materials, a blurring‐sharpening strategy is proposed to diminish noise or smooth local details on the boundaries. This generates salient features with smooth boundaries and visually pleasing structures. We compare our method with the bilateral filter and anisotropic diffusion, and demonstrate the effectiveness and efficiency of our method with several volumes in different modalities.
Photoelasticity Raycasting
Authors: Bußler M. , Ertl T. , Sadlo F.
Published: July 2015

We present a novel physically‐based method to visualize stress tensor fields. By incorporating photoelasticity into traditional raycasting and extending it with reflection and refraction, taking into account polarization, we obtain the virtual counterpart to traditional experimental polariscopes. This allows us to provide photoelastic analysis of stress tensor fields in arbitrary domains. In our model, the optical material properties, such as stress‐optic coefficient and refractive index, can either be chosen in compliance with the subject under investigation, or, in case of stress problems that do not model optical properties or that are not transparent, be chosen according to known or even new transparent materials. This enables direct application of established polariscope methodology together with respective interpretation. Using a GPU‐based implementation, we compare our technique to experimental data, and demonstrate its utility with several simulated datasets.
Interactive Visual Analysis for Vehicle Detector Data
Authors: Chen Yi‐Cheng , Wang Yu‐Shuen , Lin Wen‐Chieh , Huang Wei‐Xiang , Lin I‐Chen
Published: July 2015

Visualization of vehicle detection (VD) data is essential because the data play an important role in traffic control and policy development. Most previous works focus on visualizing trajectories obtained from global positioning system (GPS), which are detailed but less representative. In contrast, VD data report the traffic statistic at each sensing site during a time span, including speed, flow, and occupancy of each lane, which contain comprehensive traffic information for analysis. In this work, we visualize three‐year VD data of freeways in Taiwan. The visualization depicts the traffic situation at a site over time using a color‐coded chart that extends from left to right over time. The charts are vertically stacked and horizontally aligned according to VD's located mileage and data time, respectively, to provide global insight. Our system allows semantic zoom, which changes the chart appearance in a continuous manner, to enable macro‐ and micro‐ scopic visualizations. Analysts can explore events that span an area with different sizes and that persist a time span with various lengths. To ensure the feasibility of our visualization, before the system design, we conducted a study with experts who work in the national freeway bureau and the institute of transportation of Taiwan. We also showed our results to the experts after the prototype system was built. The feedback shows that our VD data visualization is helpful to traffic control and policy development.
Rationale Visualization for Safety and Security
Authors: Scheepens Roeland , Michels Steffen , van de Wetering Huub , van Wijk Jarke J.
Published: July 2015

In safety and security domains where objects of interest (OOI), such as people, vessels, or transactions, are continuously monitored, automated reasoning is required due to their sheer number and volume of information. We present a method to visually explain the rationale of a reasoning engine that raises an alarm if a certain situation is reached. Based both on evidence from heterogeneous and possibly unreliable sources, and on a domain specific reasoning structure, this engine concludes with a certain probability that, e.g., the OOI is suspected of smuggling. To support decision making, we visualize the rationale, an abstraction of the complicated reasoning structure. The evidence is displayed in a color‐coded matrix that easily reveals if and where observations contradict. In it, domain and operational experts can quickly understand and find complicated patterns and relate them to real‐world situations. Also, two groups of these experts evaluate our system through maritime use cases based on real data.
Interactive Fusion and Tracking For Multi‐Modal Spatial Data Visualization
Authors: Elshehaly M. , Gračanin D. , Gad M. , Elmongui H. G. , Matković K.
Published: July 2015

Scientific data acquired through sensors which monitor natural phenomena, as well as simulation data that imitate time‐identified events, have fueled the need for interactive techniques to successfully analyze and understand trends and patterns across space and time. We present a novel interactive visualization technique that fuses ground truth measurements with simulation results in real‐time to support the continuous tracking and analysis of spatiotemporal patterns. We start by constructing a reference model which densely represents the expected temporal behavior, and then use GPU parallelism to advect measurements on the model and track their location at any given point in time. Our results show that users can interactively fill the spatio‐temporal gaps in real world observations, and generate animations that accurately describe physical phenomena.
Visual Exploration of High‐Dimensional Data through Subspace Analysis and Dynamic Projections
Authors: Liu S. , Wang B. , Thiagarajan J. J. , Bremer P.‐T. , Pascucci V.
Published: July 2015

We introduce a novel interactive framework for visualizing and exploring high‐dimensional datasets based on subspace analysis and dynamic projections. We assume the high‐dimensional dataset can be represented by a mixture of low‐dimensional linear subspaces with mixed dimensions, and provide a method to reliably estimate the intrinsic dimension and linear basis of each subspace extracted from the subspace clustering. Subsequently, we use these bases to define unique 2D linear projections as viewpoints from which to visualize the data. To understand the relationships among the different projections and to discover hidden patterns, we connect these projections through dynamic projections that create smooth animated transitions between pairs of projections. We introduce the view transition graph, which provides flexible navigation among these projections to facilitate an intuitive exploration. Finally, we provide detailed comparisons with related systems, and use real‐world examples to demonstrate the novelty and usability of our proposed framework.
Visualization of Object‐Centered Vulnerability to Possible Flood Hazards
Authors: Cornel D. , Konev A. , Sadransky B. , Horváth Z. , Gröller E. , Waser J.
Published: July 2015

As flood events tend to happen more frequently, there is a growing demand for understanding the vulnerability of infrastructure to flood‐related hazards. Such demand exists both for flood management personnel and the general public. Modern software tools are capable of generating uncertainty‐aware flood predictions. However, the information addressing individual objects is incomplete, scattered, and hard to extract. In this paper, we address vulnerability to flood‐related hazards focusing on a specific building. Our approach is based on the automatic extraction of relevant information from a large collection of pre‐simulated flooding events, called a scenario pool. From this pool, we generate uncertainty‐aware visualizations conveying the vulnerability of the building of interest to different kinds of flooding events. On the one hand, we display the adverse effects of the disaster on a detailed level, ranging from damage inflicted on the building facades or cellars to the accessibility of the important infrastructure in the vicinity. On the other hand, we provide visual indications of the events to which the building of interest is vulnerable in particular. Our visual encodings are displayed in the context of urban 3D renderings to establish an intuitive relation between geospatial and abstract information. We combine all the visualizations in a lightweight interface that enables the user to study the impacts and vulnerabilities of interest and explore the scenarios of choice. We evaluate our solution with experts involved in flood management and public communication.
VIMTEX: A Visualization Interface for Multivariate, Time‐Varying, Geological Data Exploration
Authors: Dasgupta A. , Kosara R. , Gosink L.
Published: July 2015

Observing interactions among chemical species and microorganisms in the earth's sub‐surface is a common task in the field of geology. Bioremediation experiments constitute one such class of interactions which focus on getting rid of pollutants through processes such as carbon sequestration. The main goal of scientists’ observations is to analyze the dynamics of the chemical reactions and understand how they collectively affect the carbon content of the soil. In our work, we extract the high‐level goals of geologists and propose a visual analytics solution which helps scientists in deriving insights about multivariate, temporal behavior of these chemical species. Specifically, our key contributions are the following: i) characterization of the domain‐specific goals and their translation to exploratory data analysis tasks, ii) developing an analytical abstraction in the form of perceptually motivated screen‐space metrics for bridging the gap between the tasks and the visualization, and iii) realization of the tasks and metrics in the form of VIMTEX, which is a set of coordinated multiple views for letting scientists observe multivariate, temporal relationships in the data. We provide several examples and case studies along with expert feedback for demonstrating the efficacy of our solution.
Quantitative Measures for Cartogram Generation Techniques
Authors: Alam Md. Jawaherul , Kobourov Stephen G. , Veeramoni Sankar
Published: July 2015

Cartograms are used to visualize geographically distributed data by scaling the regions of a map (e.g., US states) such that their areas are proportional to some data associated with them (e.g., population). Thus the cartogram computation problem can be considered as a map deformation problem where the input is a planar polygonal map M and an assignment of some positive weight for each region. The goal is to create a deformed map M′, where the area of each region realizes the weight assigned to it (no cartographic error) while the overall map remains readable and recognizable (e.g., the topology, relative positions and shapes of the regions remain as close to those before the deformation as possible). Although several such measures of cartogram quality are well‐known, different cartogram generation methods optimize different features and there is no standard set of quantitative metrics. In this paper we define such a set of seven quantitative measures, designed to evaluate how faithfully a cartogram represents the desired weights and to estimate the readability of the final representation. We then study several cartogram‐generation algorithms and compare them in terms of these quantitative measures.
A Shot at Visual Vulnerability Analysis
Authors: Kerzner Ethan , Butler Lee A. , Hansen Charles , Meyer Miriah
Published: July 2015

Increasing the safety of vehicles is an important goal for vehicle manufacturers. These manufacturers often turn to simulations to understand how to improve a vehicle's design as real‐world safety tests are expensive and time consuming. Understanding the results of these simulations, however, is challenging due to the complexity of the data, which often includes both spatial and nonspatial data types. In this design study we collaborated with analysts who are trying to understand the vulnerability of military vehicles. From this design study we contribute a problem characterization, data abstraction, and task analysis for vehicle vulnerability analysis, as well as a validated and deployed tool called Shotviewer. Shotviewer links 3D spatial views with abstract 2D views to support a broad range of analysis needs. Furthermore, reflection on our design study process elucidates a strategy of view‐design parallelism for creating multiview visualizations, as well as four recommendations for conducting design studies in large organizations with sensitive data.
Persistent Homology for the Evaluation of Dimensionality Reduction Schemes
Authors: Rieck B. , Leitte H.
Published: July 2015

High‐dimensional data sets are a prevalent occurrence in many application domains. This data is commonly visualized using dimensionality reduction (DR) methods. DR methods provide e.g. a two‐dimensional embedding of the abstract data that retains relevant high‐dimensional characteristics such as local distances between data points. Since the amount of DR algorithms from which users may choose is steadily increasing, assessing their quality becomes more and more important. We present a novel technique to quantify and compare the quality of DR algorithms that is based on persistent homology. An inherent beneficial property of persistent homology is its robustness against noise which makes it well suited for real world data. Our pipeline informs about the best DR technique for a given data set and chosen metric (e.g. preservation of local distances) and provides knowledge about the local quality of an embedding, thereby helping users understand the shortcomings of the selected DR method. The utility of our method is demonstrated using application data from multiple domains and a variety of commonly used DR methods.
GraphUnit: Evaluating Interactive Graph Visualizations Using Crowdsourcing
Authors: Okoe Mershack , Jianu Radu
Published: July 2015

We present GraphUnit, a framework and online service that automates the process of designing, running and analyzing results of controlled user studies of graph visualizations by leveraging crowdsourcing and a set of evaluation modules based on a graph task taxonomy. User studies play an important role in visualization research but conducting them requires expertise and is time consuming. GraphUnit simplifies the evaluation process by allowing visualization designers to easily configure user studies for their web‐based graph visualizations, deploy them online, use Mechanical Turk to attract participants, collect user responses and store them in a database, and analyze incoming results automatically using appropriate statistical tools and graphs. We demonstrate the effectiveness of GraphUnit by replicating two published evaluation studies on network visualization, and showing that these studies could be configured in less than an hour. Finally, we discuss how GraphUnit can facilitate quick evaluations of alternative graph designs and thus encourage the frequent use of user studies to evaluate design decisions in iterative development processes.
Towards a smooth design process for static communicative node‐link diagrams
Authors: Spritzer Andre Suslik , Boy Jeremy , Dragicevic Pierre , Fekete Jean‐Daniel , Dal Sasso Freitas Carla Maria
Published: July 2015

Node‐link infographics are visually very rich and can communicate messages effectively, but can be very difficult to create, often involving a painstaking and artisanal process. In this paper we present an investigation of node‐link visualizations for communication and how to better support their creation. We begin by breaking down these images into their basic elements and analyzing how they are created. We then present a set of techniques aimed at improving the creation workflow by bringing more flexibility and power to users, letting them manipulate all aspects of a node‐link diagram (layout, visual attributes, etc.) while taking into account the context in which it will appear. These techniques were implemented in a proof‐of‐concept prototype called GraphCoiffure, which was designed as an intermediary step between graph drawing/editing software and image authoring applications. We describe how GraphCoiffure improves the workflow and illustrate its benefits through practical examples.
Plesiomorphic character states cause systematic errors in molecular phylogenetic analyses: a simulation study
Authors: Kück Patrick , Wägele J. Wolfgang
Published: July 2015

Analysis of sequence data using time‐reversible substitution models and maximum likelihood (ML) algorithms is currently the most popular method to infer phylogenies, despite the fact that results often contradict each other. Searching for sources of error we focus on a hitherto neglected feature of these methods: character polarity is usually thought to be irrelevant in ML analyses. Mechanisms that lead to wrong tree topologies were analysed at the level of split‐supporting site patterns. In simulations, plesiomorphic site patterns can be identified by comparison with known root sequences. These patterns cause some surprising effects: Using data sets generated with simulations of sequence evolution along a variety of topologies and inferring trees using the same (correct) model, we show for cases of branch‐length heterogeneity that (i) as already known, ML analyses can fail to recover the correct tree even when the correct substitution model is used, but also that (ii) plesiomorphic character states cause substantial mistakes and therefore character polarity is relevant, and (iii) accumulating chance similarities on long branches are far less misleading than plesiomorphic states accumulating on shorter branches. The artefacts occur when branch lengths are heterogeneous. The systematic errors disappear for the most part when the sites with symplesiomorphies supporting false clades are deleted from the data set. We conclude that many of the phylogenies published during the past decades may be false due to the neglected effects of symplesiomorphies.
Facilitating climate‐change‐induced range shifts across continental land‐use barriers
Authors: Robillard Cassandra M. , Coristine Laura E. , Soares Rosana N. , Kerr Jeremy T.
Published: July 2015

Climate changes impose requirements for many species to shift their ranges to remain within environmentally tolerable areas, but near‐continuous regions of intense human land use stretching across continental extents diminish dispersal prospects for many species. We reviewed the impact of habitat loss and fragmentation on species’ abilities to track changing climates and existing plans to facilitate species dispersal in response to climate change through regions of intensive land uses, drawing on examples from North America and elsewhere. We identified an emerging analytical framework that accounts for variation in species' dispersal capacities relative to both the pace of climate change and habitat availability. Habitat loss and fragmentation hinder climate change tracking, particularly for specialists, by impeding both propagule dispersal and population growth. This framework can be used to identify prospective modern‐era climatic refugia, where the pace of climate change has been slower than surrounding areas, that are defined relative to individual species' needs. The framework also underscores the importance of identifying and managing dispersal pathways or corridors through semi‐continental land use barriers that can benefit many species simultaneously. These emerging strategies to facilitate range shifts must account for uncertainties around population adaptation to local environmental conditions. Accounting for uncertainties in climate change and dispersal capabilities among species and expanding biological monitoring programs within an adaptive management paradigm are vital strategies that will improve species' capacities to track rapidly shifting climatic conditions across landscapes dominated by intensive human land use.
A hemicyanine fluorescent reactive cationic dye: synthesis and applications on wool fabrics
Authors: Zhang Wei , Zhang Yan , Cheng Yanqiu , Qin Chuanxiang , Chen Guoqiang
Published: July 2015

A novel hemicyanine fluorescent reactive cationic dye was synthesised by the reaction between the free amino group of a hemicyanine fluorescent dye and 2,3‐dibromopropionyl chloride. The dye was characterised by proton nuclear magnetic resonance spectroscopy, high‐resolution mass spectrometry, ultraviolet‐visible absorption spectrometry, and single‐photon fluorescence spectrometry. The prepared dye was applied to wool fabrics to give fluorescent orange shades. The colour fastness of the dyed wool fabrics was tested. Results show that dyed fabrics using the novel hemicyanine fluorescent reactive cationic dye could be used as fluorescent clothing.
The changing patterns of plant naturalization in Australia
Authors: Dodd Aaron J. , Burgman Mark A. , McCarthy Michael A. , Ainsworth Nigel
Published: July 2015

Aim

To identify the temporal patterns of plant naturalization in Australia, particularly the interaction between taxonomy, geographic origin and economic use.

Location

Australia.

Methods

From Australia's Virtual Herbarium, we compiled a database of information for the entire naturalized flora of Australia. We then examined the database in discrete time intervals to determine the changes in patterns of naturalized species taxonomy, geographic origin and economic use over time.

Results

Contrary to prevailing hypotheses, we found no evidence to indicate that the rate of alien flora naturalization is increasing in Australia. The number of naturalized species has grown linearly during the period 1880–2000, with the underlying rate of new species detected per thousand specimens declining over the same time period. Despite this, the diversity of both species taxonomy and geographic origin has increased over the last 120 years, leading to increased rates of growth in the total phylogenetic diversity of the Australian flora.

Main Conclusions

By classifying species according to their likely origin and economic use, we are able to infer the circumstances driving the patterns of naturalization. In particular, we identify how the contribution of individual pathways has changed since European settlement corresponding with the socio‐economic development of the continent. Our study illustrates how the changing nature of ‘high‐risk’ pathways is relevant to directing interventions such as biosecurity regulation.
Conservation of future boreal forest bird communities considering lags in vegetation response to climate change: a modified refugia approach
Authors: Stralberg Diana , Bayne Erin M. , Cumming Steven G. , Sólymos Péter , Song Samantha J. , Schmiegelow Fiona K. A.
Published: July 2015

Aim

Species and ecosystems may be unable to keep pace with rapid climate change projected for the 21st century. We evaluated an underexplored dimension of the mismatch between climate and biota: limitations to forest growth and succession affecting habitat suitability. Our objective was to inform continental‐scale conservation for boreal songbirds under disequilibria between climate, vegetation and fauna.

Location

Boreal and southern arctic ecoregions of North America.

Methods

We used forest inventory and avian survey data to classify 53 species by seral‐stage affinity and applied these to generate alternative projections of changes in species' core habitat distributions based on different vegetation lag‐time assumptions. We used our seral stage‐modified refugia approach and the Zonation algorithm to identify multispecies boreal conservation priorities over the 21st century. We evaluated the sensitivity of land rankings to seral‐stage affinity and species' weights and assessed the conservation value of the existing protected areas network compared to Zonation results.

Results

End‐of‐century projected changes in songbird distribution were reduced by up to 169% when vegetation lags were considered. Zonation land rankings based on unconstrained climate projections were concentrated at high latitudes, whereas those based on strict and modified refugia scenarios were concentrated in coastal and high‐elevation areas, as well as biome transition zones, which were fairly consistent over time and species weights. The existing protected areas network covering 14% of the study area was estimated to conserve 12–14% of baseline avian biodiversity across time periods and scenarios, compared to 16–25% for top‐ranked Zonation areas.

Main conclusions

For some boreal songbirds, limits to forest growth and succession may result in dramatic reductions in suitable habitat over the next century. Our seral stage‐adjusted approach provides conservative and efficient boreal conservation priorities anchored around climatic macrorefugia that are robust to century‐long climate change and complement the current protected areas network.
The effect of early spring grazing and dairy cow grazing intensity on particulate phosphorus losses in surface run‐off
Authors: McConnell D. A. , Doody D. G. , Elliott C. T. , Matthews D.I. , Ferris C. P.
Published: July 2015

A four‐treatment (UG‐UG, UG‐G, LG‐G and HG‐G) experiment (involving sixteen plots: 3·0 × 7·0 m) examined the effect of early spring grazing intensity on particulate phosphorus (PP) losses in surface run‐off. Ten dairy cows fitted with manure collection ‘bags’ grazed during two short‐term grazing events, Grazing‐1 (23 February) and Grazing‐2 (6 April). During Grazing‐1, two treatments remained ungrazed (UG‐), while treatments LG‐ and HG‐ were lightly grazed and heavily grazed respectively. At Grazing‐2, three treatments were grazed to a similar intensity (‐G), while one remained ungrazed (‐UG). Run‐off was generated at two and 16 days after Grazing‐1 and Grazing‐2 using rainfall simulators (40 mm h−1) and analysed for a range of P fractions. Grazing had no effect on either dissolved reactive phosphorus (DRP) concentrations or dissolved unreactive P concentrations (mean, 0·15 and 0·16 mg L−1 respectively) in run‐off. However, PP concentrations increased (P < 0·05) following Grazing‐1 (0·39, 0·53 and 0·72 mg L−1 with UG‐, LG‐ and HG‐ respectively, Day‐2 Rainfall event), with these effects still evident following Grazing‐2, especially with HG‐G (3·25 mg L−1). The risk of PP loss in run‐off can be substantially reduced by removing cows from pastures before significant damage to the soil takes place.
Historical land use by domestic grazing revealed by the soil seed bank: a case study from a natural semi‐arid grassland of NW Patagonia
Authors: Franzese J. , Ghermandi L. , Gonzalez S. L.
Published: July 2015

Livestock can affect the soil seed bank through various mechanisms associated with changes in vegetation. We sampled vegetation and seed banks of Patagonian grasslands, in areas with different historical use by grazing (exclosure, moderate use and high use) to evaluate to what extent changes in vegetation are reflected in the seed bank. We also evaluated the effect of historical grazing on horizontal spatial seed distribution by sampling under shrubs and in between plant gaps. We focused the study on functional groups, and on the palatable Poa ligularis, an indicator of grassland status. In general, the proportional changes in composition and abundance of functional groups produced in grazed sectors (relative to each exclosure) were bigger for the seed bank than for the aboveground vegetation. Impacts on seed bank were led by a decrease (moderate use), or total disappearance (high use) of perennial grasses, results clearly reflected by P. ligularis. Although shrubs were represented in vegetation, they were undetected in the seed bank through germination, probably due to the lack of the conditions required for breaking seed dormancy. Intensive grazing produced homogenization in seed spatial distribution. Our work revealed a poor contribution of the seed bank to vegetation regeneration at increasing historical use by grazing. We recommend sampling the seed bank when monitoring the conservation status of grasslands to obtain consistent management guidelines.
Assessment and management of pain in children and adolescents with bleeding disorders: a cross‐sectional study from three haemophilia centres
Authors: Rambod M. , Forsyth K. , Sharif F. , Khair K.
Published: July 2015

Introduction

Pain is a major clinical problem in patients with bleeding disorders. This study aimed to determine the level of pain and how it is managed in children and adolescents with bleeding disorders.

Methods

This cross‐sectional study was performed in three haemophilia centres (one in Shiraz and two in London).The data were collected using questions about pain management and Wong‐Baker Faces Pain Rating Scale at routine clinical review as well as attendance for bleed treatment in summer 2014.

Results

This study indicated no difference among the three haemophilia centres regarding having pain, however, a significant difference was found among them concerning the mean score of pain intensity. Among the 154 subjects, 20.8% had pain on the study day, most reporting moderate levels of pain. The study participant's most frequently described their pain as aching, dull, throbbing and stabbing. Moreover, 84.38% of pain was experienced in joints and the most common painful joints were knees, ankles, elbows, hands and hips. The most common pain relief strategies included factor administration, immobilization and rest, ice packs and analgesia. Pain was significantly associated with disease severity and age.

Conclusion

As the intensity of pain in on‐demand patients was highest, using prophylaxis treatment is suggested. Moreover, adolescent patients reported more pain; giving more self‐care information to them and their parents is recommended. Since little evidence was published for pain assessment and management in children and adolescents with bleeding disorders, more research is recommended.
Bioactive compounds and antioxidant activities of the Korean lotus leaf (Nelumbo nucifera) condiment: volatile and nonvolatile metabolite profiling during fermentation
Authors: Hwang Dongju , Charchoghlyan Haykuhi , Lee Jong Suk , Kim Myunghee
Published: July 2015

Recent studies have shown that lotus (Nelumbo nucifera) leaf has various pharmacological effects. However, there have been no scientific investigations into these leaves as a fermented crude liquid. This study compared the in vitro antioxidant capacity of lotus leaf‐fermented broth (LLFB) with that of 57° Brix sugar broth (SB) as a control over a period of 6 months based on 1,1‐diphenyl‐2‐picrylhydrazyl radical scavenging activity, ferric ion reducing power, superoxide dismutase‐like activity, tyrosinase inhibition and nitrite scavenging activity. The dominant species during fermentation process were Leuconostoc lactis and Saccharomyces cerevisiae for LLFB. A total of thirty‐six metabolites such as alkaloids, fatty acids, organic acids, phenolics, sugar and sugar derivatives, ethyl esters and monoterpenoids differed between SB and LLFB using gas chromatography–mass spectrometry. Meanwhile, nine volatile compounds in LLFB contributed pleasant, slightly sweetish and fruity odour of condiment and sensory evaluation score of 4.06 ± 1.52 in the proportion of 1:9 LLFB/water.
Bioactive properties of enzymatic hydrolysates from abdominal skin gelatin of yellowfin tuna (Thunnus albacares)
Authors: Han Yuna , Byun Sang‐Hun , Park Joung‐Hyun , Kim Seon‐Bong
Published: July 2015

Gelatin (90.6 ± 0.1%) was optimally prepared by response surface methodology from yellowfin tuna (Thunnus albacares, YT) abdominal skin. To investigate bioactive properties of enzymatic hydrolysates from the abdominal skin gelatin (ASG), ASG was hydrolysed with alcalase, protamex, neutrase and flavourzyme as affected by hydrolysis time. Antioxidant, nitrite scavenging and angiotensin‐I converting enzyme (ACE) inhibitory activities of the hydrolysates were determined. Antioxidant activities of the hydrolysates were found through linoleic acid peroxidation inhibitory effects. Alcalase‐derived hydrolysates (AHs) were more effective than others in metal ions chelating, superoxide anion scavenging and hydroxyl radical scavenging activities (P < 0.05). AHs showed significantly stronger nitrite scavenging activities (44.4–60.7%) than others (P < 0.05). Fraction A from AH showed strong ACE inhibitory activity (IC50 of 0.75 mg mL−1). These results suggest that YT ASG and its enzymatic hydrolysates could be functional food and/or pharmaceutical ingredients with potent antioxidant, anticarcinogenic and antihypertensive benefits.