bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Shot at Visual Vulnerability Analysis
Authors: Kerzner Ethan , Butler Lee A. , Hansen Charles , Meyer Miriah 
Published: July 2015

AbstractIncreasing 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

AbstractHigh‐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

AbstractWe 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

AbstractNode‐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

AbstractAnalysis 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

AbstractClimate 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.
The changing patterns of plant naturalization in Australia
Authors: Dodd Aaron J. , Burgman Mark A. , McCarthy Michael A. , Ainsworth Nigel 
Published: July 2015

AbstractAimTo identify the temporal patterns of plant naturalization in Australia, particularly the interaction between taxonomy, geographic origin and economic use.LocationAustralia.MethodsFrom 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.ResultsContrary 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 ConclusionsBy 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

AbstractAimSpecies 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.LocationBoreal and southern arctic ecoregions of North America.MethodsWe 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.ResultsEnd‐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 conclusionsFor 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

AbstractA 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

AbstractLivestock 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

IntroductionPain 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.MethodsThis 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.ResultsThis 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.ConclusionAs 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

SummaryRecent 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

SummaryGelatin (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.
Properties of extruded whole grain cereals and pseudocereals flours
Authors: Robin Frédéric , Théoduloz Christine , Srichuwong Sathaporn 
Published: July 2015

SummaryCommon cereals such as wheat are widely used worldwide in extruded products. Nevertheless, other locally available grains would be beneficial for local consumers regarding taste preference, nutritional needs and sustainability. Locally available cereals, that is millet, teff, sorghum and pseudocereals, that is quinoa and amaranth flours were extruded at the same processing conditions, and the resulting properties were compared to those of extruded refined wheat flour. Amaranth flour contained the highest protein content (16%). Sorghum was the highest in calories because of its high lipid content (10%). The extrusion process greatly increased a water solubility index (WSI) of amaranth from 11% to 61%, while the WSI level of quinoa was almost not affected (WSI of 4%). The expansion properties varied differently among grain types. These grains had a sectional expansion index (SEI) ranging between 11 and 13, which could not achieve the performance of the refined wheat (SEI of 22). The lowest expansion was observed for amaranth flour which contained the lowest starch content. Sorghum extrudates, interestingly, provided comparable stress at rupture value to that of wheat. For the mechanical properties, none of these local grains could fully replace refined wheat at the employed extrusion conditions.
A multiplex method for detection of glucose‐6‐phosphate dehydrogenase (G6PD) gene mutations
Authors: Zhang L. , Yang Y. , Liu R. , Li Q. , Yang F. , Ma L. , Liu H. , Chen X. , Yang Z. , Cui L. , He Y. 
Published: July 2015

SummaryIntroductionGlucose‐6‐phosphate dehydrogenase (G6PD) deficiency is the most common human enzyme defect caused by G6PD gene mutations. This study aimed to develop a cost‐effective, multiplex, genotyping method for detecting common mutations in the G6PD gene.MethodsWe used a SNaPshot approach to genotype multiple G6PD mutations that are common to human populations in South‐East Asia. This assay is based on multiplex PCR coupled with primer extension reactions. Different G6PD gene mutations were determined by peak retention time and colors of the primer extension products.ResultsWe designed PCR primers for multiplex amplification of the G6PD gene fragments and for primer extension reactions to genotype 11 G6PD mutations. DNA samples from a total of 120 unrelated G6PD‐deficient individuals from the China–Myanmar border area were used to establish and validate this method. Direct sequencing of the PCR products demonstrated 100% concordance between the SNaPshot and the sequencing results.ConclusionThe SNaPshot method offers a specific and sensitive alternative for simultaneously interrogating multiple G6PD mutations.