bluuebunny/crossref_metadata_2025 huggingface dataset:
Bacteriophage-derived CHAP domain protein, P128, kills Staphylococcus cells by cleaving interpeptide cross-bridge of peptidoglycan
Authors: Sundarrajan Sudarson , Raghupatil Junjappa , Vipra Aradhana , Narasimhaswamy Nagalakshmi , Saravanan Sanjeev , Appaiah Chemira , Poonacha Nethravathi , Desai Srividya , Nair Sandhya , Bhatt Rajagopala Narayana , Roy Panchali , Chikkamadaiah Ravisha , Durgaiah Murali , Sriram Bharathi , Padmanabhan Sriram , Sharma Umender
Published: July 2014

P128 is an anti-staphylococcal protein consisting of the Staphylococcus aureus phage-K-derived tail-associated muralytic enzyme (TAME) catalytic domain (Lys16) fused with the cell-wall-binding SH3b domain of lysostaphin. In order to understand the mechanism of action and emergence of resistance to P128, we isolated mutants of Staphylococcus spp., including meticillin-resistant Staphylococcus aureus (MRSA), resistant to P128. In addition to P128, the mutants also showed resistance to Lys16, the catalytic domain of P128. The mutants showed loss of fitness as shown by reduced rate of growth in vitro. One of the mutants tested was found to show reduced virulence in animal models of S. aureus septicaemia suggesting loss of fitness in vivo as well. Analysis of the antibiotic sensitivity pattern showed that the mutants derived from MRSA strains had become sensitive to meticillin and other β-lactams. Interestingly, the mutant cells were resistant to the lytic action of phage K, although the phage was able to adsorb to these cells. Sequencing of the femA gene of three P128-resistant mutants showed either a truncation or deletion in femA, suggesting that improper cross-bridge formation in S. aureus could be causing resistance to P128. Using glutathione S-transferase (GST) fusion peptides as substrates it was found that both P128 and Lys16 were capable of cleaving a pentaglycine sequence, suggesting that P128 might be killing S. aureus by cleaving the pentaglycine cross-bridge of peptidoglycan. Moreover, peptides corresponding to the reported cross-bridge of Staphylococcus haemolyticus (GGSGG, AGSGG), which were not cleaved by lysostaphin, were cleaved efficiently by P128. This was also reflected in high sensitivity of S. haemolyticus to P128. This showed that in spite of sharing a common mechanism of action with lysostaphin, P128 has unique properties, which allow it to act on certain lysostaphin-resistant Staphylococcus strains.
A food‐borne outbreak of gastroenteritis due to genotype G1P[8] rotavirus among adolescents in Japan
Authors: Mizukoshi Fuminori , Kuroda Makoto , Tsukagoshi Hiroyuki , Sekizuka Tsuyoshi , Funatogawa Keiji , Morita Yukio , Noda Masahiro , Katayama Kazuhiko , Kimura Hirokazu
Published: July 2014

Six high school students in Tochigi prefecture, Japan, developed gastroenteritis after eating at a pork cutlet shop. Molecular epidemiologic analyses showed that the causative agent was genotype G1P[8] rotavirus (RV), this being detected in stool samples from both the patients and the asymptomatic food handlers. The detected RV strains were closely related genetically. The only uncooked food that all victims had eaten was raw sliced cabbage. These findings results suggest that uncooked foods contaminated with RV may be sources of infectious gastroenteritis in adolescents.
Improving abundance estimation by combining capture–recapture and occupancy data: example with a large carnivore
Authors: Blanc Laetitia , Marboutin Eric , Gatti Sylvain , Zimmermann Fridolin , Gimenez Olivier
Published: July 2014

Abundance is a key quantity for conservation and management strategies but remains challenging to assess in the field. Capture–recapture (CR) methods are often used to estimate abundance while correcting for imperfect detection, but these methods are costly. Occupancy, sometimes considered as a surrogate for abundance, is estimated through the collection of presence/absence data and is less costly while allowing gathering of information at a large spatial scale.

Building on the recent pieces of work on the combination of different data sources, we showed how abundance data can be complemented by presence/absence data and can be analysed conjointly to improve abundance estimates. Our approach relies on a hierarchical model that makes explicit the link between the abundance and occupancy state variables while formally accounting for imperfect detection.

We used a population of Eurasian lynx in France monitored via camera traps and a collection of presence signs as an illustration of our approach.

Synthesis and applications.We combined capture–recapture and occupancy data and demonstrated that we can efficiently improve abundance estimates. Our method can be used by managers when estimates of trends in abundance lack power due to sparse data collected during an intensive survey, by simply integrating data collected during non‐systematic survey. Furthermore, combining these two sampling procedures makes full use of all available data and allows the development of conservation and management strategies based on precise abundance estimates. Overall, the combination of different data sources in an integrated statistical framework has great potential, especially for elusive species.
Market Integration and Spatial Price Transmission in Niger Grain Markets
Authors: Zakari Seydou , Ying Liu , Song Baohui
Published: July 2014

This paper investigates price transmission from international and regional markets to Niger domestic grain markets using monthly wholesale prices. Cointegration and error correction models were employed to analyze the degree of price transmission. Tests of causality were also performed. In general, the results showed that grain markets in Niger respond to negative and positive shocks in regional and international markets differently. Maize and rice markets have high speed of adjustments to world prices compared to millet and sorghum markets. The speed of adjustment of prices to the long‐run equilibrium varies between 30 percent, 35 percent, 48 percent and 40 percent respectively for millet, sorghum, maize and rice prices. Nigeria, Burkina‐Faso, Mali, Togo and Vietnam markets have shown significant transmission in Niger markets. Supply and demand shocks in these markets will definitely affect Niger food prices. Based on this analysis, we suggest that Niger should develop a proper trade policy with its neighboring countries to facilitate regional market integration. This will enable Niger to import cereals from regional surplus‐producing areas to supply its food shock regions to reduce the negative impacts of price shocks on households. For rice, Niger should encourage local production to limit high dependence on international markets.
Revisiting the Finance–Growth Nexus in Sub‐Saharan Africa: Results from Error Correction‐based Panel Cointegration Tests
Authors: Walle Yabibal M.
Published: July 2014

This paper re‐examines the long‐run finance‐growth nexus in sub‐Saharan Africa (SSA) using data from 17 countries over the period 1975–2005. We apply error correction‐based panel cointegration tests that take into account cross‐sectional dependence among countries. Our results — unlike a previous study using the same data — indicate the existence of a long‐run relationship between financial and economic development in SSA countries. Moreover, our results clearly show that the long‐run causality runs from financial to economic development, although a muted support for the reverse causal impact is observed when financial development is measured by the percentage of liquid liabilities in GDP. The estimated long‐run parameters measuring the finance–growth link are positive and statistically significant. Therefore, our results strongly support policies aimed at developing the financial sector in SSA in order to promote long‐run economic development.
Electricity Consumption–Economic Growth–CO2 Emissions Nexus in Sub‐Saharan Africa: Evidence from Panel Cointegration
Authors: Gao Jing , Zhang Lei
Published: July 2014

This study explores the causal relationship among electricity consumption, economic growth and CO2 emissions for a group of 14 sub‐Sahara African (SSA) countries from 1980 to 2009 using panel cointegration and panel vector error correction modelling methods. The findings demonstrate that in the long run electricity consumption has a statistically significant positive impact on CO2 emissions. The results also reveal that the inverted U‐shaped Environmental Kuznets Curve (EKC) hypothesis exists in the SSA countries' case. The panel causality tests indicate that there is short‐run unidirectional causality running from economic growth to CO2 emissions and electricity consumption respectively. Simultaneously, there is long‐run bidirectional causality between electricity consumption and economic growth, electricity consumption and CO2 emissions, economic growth and CO2 emissions. Depending on the results, relevant policies can be initiated without negatively affecting economic growth.
Does Trade with China Have an Impact on African Countries' Growth?
Authors: Kummer‐Noormamode Sabina
Published: July 2014

The results of growth regressions using panel data econometric models for 37 African countries from 1985 to 2012 show that trade with China has had a positive impact on African GDP, but only during the final decade of that period. They also suggest that during this period, trade with China tended to have more impact on African economies than trade with the EU. Furthermore, several robustness tests are performed and confirm these conclusions.
Cities in Contemporary Capitalism
Authors: Krätke Stefan
Published: July 2014

This article outlines essential concepts of the political economy approach of urban research and offers critical modifications and clarifications to some of its contentions concerning the functioning of cities as ‘strategic places’ of capital accumulation. The interrelations between contemporary capitalism and urban economic development are discussed at the scale of a transnationally extended urban system. Based on the general context of the global economic downturn, I focus on the role of cities in distinct circuits of capital, the switching of capital flows within the urban system and the different functional roles of cities within the world city network that interconnects cities both in the global North and South. I call into question the established focus of urban economic research on the role of cities as financial and service centres, arguing that cities might redirect their economic development trajectories towards ‘real economy’ activities, in contrast to relying on the disastrous development model of finance‐dominated capitalism.
Using inter‐institutional practice variation to understand the risks and benefits of routine labour induction at 41+0 weeks
Authors: Hutcheon JA , Harper S , Strumpf EC , Lee L , Marquette G
Published: July 2014

Objective

To evaluate the risks and benefits of routine labour induction at 41+0 weeks' gestation for mother and newborn.

Design

Population‐based retrospective cohort study of inter‐institutional variation in labour induction practices for women at or beyond 41+0 weeks' gestation.

Population

Women in British Columbia, Canada, who remained pregnant ≥41+0 weeks and delivered at one of the province's 42 hospitals with >50 annual deliveries, 2008–2012 (n = 14 627).

Methods

The proportion of women remaining pregnant a week or more past the expected delivery date who were induced at 41+0 or 41+1 weeks' gestation for an indication of ‘post‐dates’ was calculated for each institution. We used instrumental variable analysis (using the institutional rate of labour induction at 41+0 weeks as the instrument) to estimate the effect of labour induction on maternal and neonatal health outcomes.

Main outcome measures

Caesarean delivery, instrumental delivery, post‐partum haemorrhage, 3rd or 4th degree lacerations, macrosomia, neonatal intensive care unit admission, and 5‐minute Apgar score <7.

Results

Institutional rates of labour induction at 41+0 weeks ranged from 14.3 to 46%. Institutions with higher (≥30%) and average (20–29.9%) induction rates did not have significantly different rates of caesarean delivery, instrumental delivery, or other maternal or neonatal outcomes than institutions with lower induction rates (<20%). Instrumental variable analyses also demonstrated no significantly increased (or decreased) risk of caesarean delivery (0.69 excess cases per 100 pregnancies [95% CI −10.1, 11.5]), instrumental delivery (8.9 per 100 [95% CI −2.3, 20.2]), or other maternal or neonatal outcomes in women who were induced (versus not induced).

Conclusions

Within the current range of clinical practice, there was no evidence that differential use of routine induction at 41+0 weeks affected maternal or neonatal health outcomes.
Surge Capacity: Analysis of Census Fluctuations to Estimate the Number of Intensive Care Unit Beds Needed
Authors: Olafson Kendiss , Ramsey Clare , Yogendran Marina , Fransoo Randall , Chrusch Carla , Forget Evelyn , Garland Allan
Published: July 2014

Objective

To compare methods of characterizing intensive care unit (ICU) bed use and estimate the number of beds needed.

Study Setting

Three geographic regions in the Canadian province of Manitoba.

Study Design

Retrospective analysis of population‐based data from April 1, 2000, to March 31, 2007.

Methods

We compared three methods to estimateICUbed requirements. Method 1 analyzed yearly patient‐days. Methods 2 and 3 analyzed day‐to‐day fluctuations in patient census; these differed by whether each hospital needed to independently fulfill its own demand or this resource was shared across hospitals.

Principal Findings

Three main findings were as follows: (1) estimates based on yearly average usage generally underestimated the number of beds needed compared to analysis of fluctuations in census, especially in the smaller regions where underestimation ranged 25–58 percent; (2) 4–29 percent fewer beds were needed if it was acceptable for demand to exceed supply 18 days/year, versus 4 days/year; and (3) 13–36 percent fewer beds were needed if hospitals within a region could effectively shareICUbeds.

Conclusions

Compared to using yearly averages, analyzing day‐to‐day fluctuations in patient census gives a more accurate picture ofICUbed use. Failing to provide adequate “surge capacity” can lead to demand that frequently and severely exceeds supply.
Contrasting assignment of migratory organisms to geographic origins using long‐term versus year‐specific precipitation isotope maps
Authors: Vander Zanden Hannah B. , Wunder Michael B. , Hobson Keith A. , Van Wilgenburg Steven L. , Wassenaar Leonard I. , Welker Jeffrey M. , Bowen Gabriel J.
Published: July 2014

As a result of predictable large‐scale continental gradients in the isotopic composition of precipitation, stable isotopes of hydrogen (δ2H) are useful endogenous markers for delineating long‐distance movements of animals. Models to predict patterns of δ2H in precipitation (δ2Hp), and consequently determine likely geographic origin of migratory animals, have traditionally used static, amount‐weighted long‐term average values of δ2Hp over the growing season. However, animal tissues reflect H incorporated from food webs that integrate precipitation over a single year's growing season or portions thereof. Inter‐annual variation in precipitation and other climatic variables may lead to deviations from predictions derived from long‐term mean precipitation isotopic values and could therefore lead to assignment errors for specific years and locations that are atypical.

We examined whether using biologically relevant short‐term δ2Hp isoscapes can improve estimates of geographic origin in comparison with long‐term isoscapes. Using δ2H data from known‐origin tissues of two migratory organisms in North America and Europe, we compared the accuracy, precision and similarity of assigned origins using both short‐ and long‐term δ2Hp isoscapes.

Relative to long‐term δ2Hp isoscapes, using short‐term isoscapes for assignment often resulted in dissimilar regions of likely origin but did not significantly improve accuracy or precision. This was likely due to reduced spatial coverage in the data used to generate the short‐term δ2Hp isoscapes.

We suggest that continued efforts to collect precipitation isotope data with a large spatiotemporal range will benefit future research on incorporating temporal variation in the amount and isotopic composition of precipitation into geospatial assignment models.
Applying computer‐aided photo‐identification to messy datasets: a case study of Thornicroft's giraffe (Giraffa camelopardalis thornicrofti)
Authors: Halloran Kelly M. , Murdoch James D. , Becker Matthew S.
Published: July 2014

Digital photography enables researchers to rapidly compile large quantities of data from individually identifiable animals, and computer software improves the management of such large datasets while aiding the identification process. Wild‐ID software has performed well with uniform datasets controlling for angle and portion of the animal photographed; however, few datasets are collected under such controlled conditions. We examined the effectiveness of Wild‐ID in identifying individual Thornicroft's giraffe from a dataset of photographs (n = 552) collected opportunistically in the Luangwa Valley, Zambia from March to October 2009. We assessed the programme's accuracy in correctly identifying individuals and the effect of five image quality factors on identification success: blurriness, background type and complexity, amount of sky and the presence of other giraffe. The programme correctly identified individuals in 71.6% of photographs. Background complexity was the only significant variable affecting identification success and removing background imagery reduced identification error by 52.8% (from 28.4 to 13.4%). Our results indicate higher levels of error than previously reported for Wild‐ID. However, they also suggest the programme is an effective tool for quickly identifying individuals in large field datasets, especially if photograph backgrounds are removed beforehand and postanalysis visual verification is performed.
Frontiers as dilemma: the incompatible desires for tea production in southwest China
Authors: Hung Po‐Yi
Published: July 2014

In this paper, I argue that frontiers are dilemmas composed of multiple dualities, be they exclusive and inclusive powers, connected space and national periphery, or modernity and primitiveness. These dilemmas, in consequence, become the mechanism to create a leeway for the state to ‘tailor’ different meanings of frontier to meet the contingent market demands. I use tea production on China's southwest frontier as an example to demonstrate that dilemma is not an end result, but a mechanism to rearticulate the relationship among frontier, the state and the market economy. Specifically, I argue that dilemmas on China's southwest frontier have been forged by the Chinese state with its incompatible desires between ‘modernisation’ and ‘primitiveness’ of the tea landscapes in Yunnan, a province on China's southwest frontier. Meanwhile, the incompatible desires and the resulting dilemmas on China's southwest frontier have further mobilised the state to flexibly rework its power to reconstruct the frontier to meet contingent market demand. Based on the shifting meanings of tea landscapes, the state has flexibly ‘shuttled through’ the dilemmas between development of modernisation and preservation of primitiveness on the frontier.
Intramammary infusion of an Enterococcus faecium SF68 preparation promoted the involution of drying off Holstein cows partly related to neutrophil‐associated matrix metalloproteinase 9
Authors: Tiantong Attapol , Peng Hsing‐Yi , Chen Shuen‐Ei , Piamya Piya , Liu Wen‐Bor , Chen Ming‐Tsao , Yu Chi , Nagahata Hajime , Chang Chai‐Ju
Published: July 2014

A problem for dairy cows following milk stasis is to cope with a high risk of intramammary infection and there is a need to initiate an extensive renewal of secretory modules in mammary glands so that milk production in next lactation may be optimized. We recently reported that ultrasonicated Enterococcus faecium SF68 (SF68) is compatible with cow mammary glands and an enhancer of innate immunity during the immediate post‐milk stasis period. The current study further examines the concomitant effect of ultrasonicated SF68 on mammary tissue remodeling. Four Holstein cows each received intramammary infusions of regular antibiotic dry‐cow formula (positive control) and two different doses of SF68 in different quarters. Analyses of individual quarter secretion samples showed faster neutrophil infiltration, earlier modifications in protein composition, including caseins and lactoferrins, as well as more prompt elevation of the specific unit of 92‐kDa matrix metalloproteinase 9 (MMP9) in SF68‐infused quarters compared to the positive controls. Intramammary infusion of ultrasonicated SF68 seems able to accelerate the regression of mammary synthetic capacity and potentiate the breakdown of glandular extracellular matrix, indicating a more efficient mammary gland involution. Correlation analyses imply that the ability of ultrasonicated SF68 to induce faster neutrophil chemotaxis and the associated MMP9 release is partly responsible.
Targeting the histone orthography of cancer: drugs for writers, erasers and readers
Authors: Simó‐Riudalbas Laia , Esteller Manel
Published: July 2014

Gene expression is dynamically controlled by epigenetics through post‐translational modifications of histones, chromatin‐associated proteins and DNA itself. All these elements are required for the maintenance of chromatin structure and cell identity in the context of a normal cellular phenotype. Disruption of epigenetic regulation is a common event in human cancer. Here, we review the key protein families that control epigenetic signalling through writing, erasing or reading specific post‐translational modifications. By exploiting the leading role of epigenetics in tumour development and the reversibility of epigenetic modifications, promising novel epigenetic‐based therapies are being developed. In this article, we highlight the emerging low MW inhibitors targeting each class of chromatin‐associated protein, their current use in preclinical and clinical trials and the likelihood of their being approved in the near future.

Linked Articles

This article is part of a themed section on Epigenetics and Therapy. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2015.172.issue‐11
Identification of novel insulin mimetic drugs by quantitative total internal reflection fluorescence (TIRF) microscopy
Authors: Lanzerstorfer Peter , Stadlbauer Verena , Chtcheglova Lilia A , Haselgrübler Renate , Borgmann Daniela , Wruss Jürgen , Hinterdorfer Peter , Schröder Klaus , Winkler Stephan M , Höglinger Otmar , Weghuber Julian
Published: July 2014

Background and Purpose

Insulin stimulates the transport of glucose in target tissues by triggering the translocation of glucose transporter 4 (GLUT4) to the plasma membrane. Resistance to insulin, the major abnormality in type 2 diabetes, results in a decreased GLUT4 translocation efficiency. Thus, special attention is being paid to search for compounds that are able to enhance this translocation process in the absence of insulin.

Experimental Approach

Total internal reflection fluorescence (TIRF) microscopy was applied to quantify GLUT4 translocation in highly insulin‐sensitive CHO‐K1 cells expressing a GLUT4‐myc‐GFP fusion protein.

Key Results

Using our approach, we demonstrated GLUT4 translocation modulatory properties of selected substances and identified novel potential insulin mimetics. An increase in the TIRF signal was found to correlate with an elevated glucose uptake. Variations in the expression level of the human insulin receptor (hInsR) showed that the insulin mimetics identified stimulate GLUT4 translocation by a mechanism that is independent of the presence of the hInsR.

Conclusions and Implications

Taken together, the results indicate that TIRF microscopy is an excellent tool for the quantification of GLUT4 translocation and for identifying insulin mimetic drugs.
Guidance for peptide vaccines for the treatment of cancer
Authors: Yamaguchi Yoshiyuki , Yamaue Hiroki , Okusaka Takuji , Okuno Kiyotaka , Suzuki Hiroyuki , Fujioka Tomoaki , Otsu Atsushi , Ohashi Yasuo , Shimazawa Rumiko , Nishio Kazuto , Furuse Junji , Minami Hironobu , Tsunoda Takuya , Hayashi Yuzo , Nakamura Yusuke ,   The Committee of Guidance for Peptide Vaccines for the Treatment of Cancer, The Japanese Society for Biological Therapy
Published: July 2014

Recent progress in fundamental understanding of tumor immunology has opened a new avenue of cancer vaccines. Currently, the development of new cancer vaccines is a global topic and has attracted attention as one of the most important issues in Japan. There is an urgent need for the development of guidance for cancer vaccine clinical studies in order to lead to drug development. Peptide vaccines characteristically have the effect of indirectly acting against cancer through the immune system – a mechanism of action that clearly differs from anticancer drugs that exert a direct effect. Thus, the clinical development of cancer peptide vaccines should be planned and implemented based on the mechanism of action, which differs significantly from conventional anticancer drug research. The Japanese Society for Biological Therapy has created and published Guidance for peptide vaccines for the treatment of cancer as part of its mission and responsibilities towards cancer peptide vaccine development, which is now pursued globally. We welcome comments from regulators and business people as well as researchers in this area.
An Integrative Theory of Numerical Development
Authors: Siegler Robert S. , Lortie‐Forgues Hugues
Published: July 2014

Understanding of numerical development is growing rapidly, but the volume and diversity of findings can make it difficult to perceive any coherence in the process. The integrative theory of numerical development posits that a coherent theme does exist—progressive broadening of the set of numbers whose magnitudes can be accurately represented—and that this theme unifies numerical development from infancy to adulthood. From this perspective, development of numerical representations involves four major acquisitions: (a) representing magnitudes of nonsymbolic numbers increasingly precisely, (b) linking nonsymbolic to symbolic numerical representations, (c) extending understanding to increasingly large whole numbers, and (d) extending understanding to all rational numbers. Thus, the mental number line expands rightward to encompass larger whole numbers, leftward to encompass negatives, and interstitially to include fractions and decimals.
Stability of Dissipation Elements: A Case Study in Combustion
Authors: Gyulassy A. , Bremer P.T. , Grout R. , Kolla H. , Chen J. , Pascucci V.
Published: July 2014

Recently, dissipation elements have been gaining popularity as a mechanism for measurement of fundamental properties of turbulent flow, such as turbulence length scales and zonal partitioning. Dissipation elements segment a domain according to the source and destination of streamlines in the gradient flow field of a scalar function f : → ℝ. They have traditionally been computed by numerically integrating streamlines from the center of each voxel in the positive and negative gradient directions, and grouping those voxels whose streamlines terminate at the same extremal pair. We show that the same structures map well to combinatorial topology concepts developed recently in the visualization community. Namely, dissipation elements correspond to sets of cells of the Morse‐Smale complex. The topology‐based formulation enables a more exploratory analysis of the nature of dissipation elements, in particular, in understanding their stability with respect to small scale variations. We present two examples from combustion science that raise significant questions about the role of small scale perturbation and indeed the definition of dissipation elements themselves.
Visualization of Medicine Prescription Behavior
Authors: van der Corput Paul , Arends Johan , van Wijk Jarke J.
Published: July 2014

Medicine prescriptions play an important role in medical treatments. More insight in medicine prescription behavior can lead to more efficient and effective treatments, as well as reflection on prescription behavior for specific physicians, types of medicines, or classes of patients. Most current medical visualization systems show health data only from the perspective of patients, whereas to understand prescription behavior multiple perspectives are relevant. We present a new approach to visualize prescription data from four different perspectives: physician, patient, medicine, and prescription. Information about physicians, patients, and medicines is shown in three tables; relations between selected items in these tables are shown using custom glyphs and histograms. These tables can also be used to define selections of prescriptions which can be compared to each other by showing a variety of metrics. This enables physicians and possibly other stakeholders to perform a wide variety of queries and inspections, while the use of familiar metaphors, such as tables and histograms, enables them to use the system in short time. This was confirmed by an evaluation session with six neurologists from an institute of epileptology. Our system is tailored to medicine prescription data, but we argue that the underlying pattern in the data is ubiquitous, and that hence our approach can be useful for many other cases where A provides B to C.
Visualizing Validation of Protein Surface Classifiers
Authors: Sarikaya A. , Albers D. , Mitchell J. , Gleicher M.
Published: July 2014

Many bioinformatics applications construct classifiers that are validated in experiments that compare their results to known ground truth over a corpus. In this paper, we introduce an approach for exploring the results of such classifier validation experiments, focusing on classifiers for regions of molecular surfaces. We provide a tool that allows for examining classification performance patterns over a test corpus. The approach combines a summary view that provides information about an entire corpus of molecules with a detail view that visualizes classifier results directly on protein surfaces. Rather than displaying miniature 3D views of each molecule, the summary provides 2D glyphs of each protein surface arranged in a reorderable, small‐multiples grid. Each summary is specifically designed to support visual aggregation to allow the viewer to both get a sense of aggregate properties as well as the details that form them. The detail view provides a 3D visualization of each protein surface coupled with interaction techniques designed to support key tasks, including spatial aggregation and automated camera touring. A prototype implementation of our approach is demonstrated on protein surface classifier experiments.
Visualizing Multidimensional Data with Glyph SPLOMs
Authors: Yates A. , Webb A. , Sharpnack M. , Chamberlin H. , Huang K. , Machiraju R.
Published: July 2014

Scatterplot matrices or SPLOMs provide a feasible method of visualizing and representing multi‐dimensional data especially for a small number of dimensions. For very high dimensional data, we introduce a novel technique to summarize a SPLOM, as a clustered matrix of glyphs, or a Glyph SPLOM. Each glyph visually encodes a general measure of dependency strength, distance correlation, and a logical dependency class based on the occupancy of the scatterplot quadrants. We present the Glyph SPLOM as a general alternative to the traditional correlation based heatmap and the scatterplot matrix in two examples: demography data from the World Health Organization (WHO), and gene expression data from developmental biology. By using both, dependency class and strength, the Glyph SPLOM illustrates high dimensional data in more detail than a heatmap but with more summarization than a SPLOM. More importantly, the summarization capabilities of Glyph SPLOM allow for the assertion of “necessity” causal relationships in the data and the reconstruction of interaction networks in various dynamic systems.
Sparse Representation and Visualization for Direct Numerical Simulation of Premixed Combustion
Authors: Oster Timo , Lehmann Dirk J. , Fru Gordon , Theisel Holger , Thévenin Dominique
Published: July 2014

Direct Numerical Simulations of premixed combustion produce terabytes of raw data, which are prohibitively large to be stored, and have to be analyzed and visualized. A simultaneous and integrated treatment of data storage, data analysis and data visualization is required. For this, we introduce a sparse representation tailored to DNS data which can directly be used for both analysis and visualization. The method is based on the observation that most information is located in narrow‐band regions where the chemical reactions take place, but these regions are not well defined. An approach for the visual investigation of feature surfaces of the scalar fields involved in the simulation is shown as a possible application. We demonstrate our approach on multiple real datasets.
Object Repositioning Based on the Perspective in a Single Image
Authors: Iizuka S. , Endo Y. , Hirose M. , Kanamori Y. , Mitani J. , Fukui Y.
Published: July 2014

We propose an image editing system for repositioning objects in a single image based on the perspective of the scene. In our system, an input image is transformed into a layer structure that is composed of object layers and a background layer, and then the scene depth is computed from the ground region that is specified by the user using a simple boundary line. The object size and order of overlapping are automatically determined during the reposition based on the scene depth. In addition, our system enables the user to move shadows along with objects naturally by extracting the shadow mattes using only a few user‐specified scribbles. Finally, we demonstrate the versatility of our system through applications to depth‐of‐field effects, fog synthesis and 3D walkthrough in an image.
‘Trafficking’ or ‘personal use’: Do people who regularly inject drugs understand Australian drug trafficking laws?
Authors: Hughes Caitlin E. , Ritter Alison , Cowdery Nicholas , Sindicich Natasha
Published: July 2014

Introduction and Aims

Legal thresholds for drug trafficking, over which possession of an illicit drug is deemed ‘trafficking’ as opposed to ‘personal use’, are employed in all Australian states and territories excepting Queensland. In this paper, we explore the extent to which people who regularly inject drugs understand such laws.

Design and Methods

Participants from the seven affected states/territories in the 2012 Illicit Drug Reporting System (n = 823) were asked about their legal knowledge of trafficking thresholds: whether, if arrested, quantity possessed would affect legal action taken; and the quantities of heroin, methamphetamine, cocaine and cannabis that would constitute an offence of supply. Data were compared against the actual laws to identify the accuracy of knowledge by drug type and state, and sociodemographics, use and purchasing patterns related to knowledge.

Results

Most Illicit Drug Reporting System participants (77%) correctly said that quantity possessed would affect charge received. However, only 55.8% nominated any specific quantity that would constitute an offence of supply, and of those 22.6% nominated a wrong quantity, namely a quantity that was larger than the actual quantity for supply (this varied by state and drug).

Discussion and Conclusions

People who regularly inject drugs have significant gaps in knowledge about Australian legal thresholds for drug trafficking, particularly regarding the actual threshold quantities. This suggests that there may be a need to improve education for this population. Necessity for accurate knowledge would also be lessened by better design of Australian drug trafficking laws. [Hughes CE, Ritter A, Cowdery N, Sindicich N. ‘Trafficking’ or ‘personal use’: Do people who regularly inject drugs understand Australian drug trafficking laws? Drug Alcohol Rev 2014;33:658‐666]
Achondroplasia and brain stem dysfunction
Authors: Menezes Arnold H
Published: July 2014

This commentary is on the original article by Bosemani et al. on pages 1085–1092 of this issue.
Multiple environmental stressors increase the realised niche breadth of a forest‐dwelling fish
Authors: White Richard S. A. , McHugh Peter A. , Glover Chris N. , McIntosh Angus R.
Published: July 2014

Understanding the determinants of species' niche breadth is important due to the negative relationship between niche breadth and extinction probability. Species tolerant to extremely harsh abiotic conditions (e.g. low pH or hypoxia) often have relatively small realised niches due to a trade‐off between abiotic and biotic stress tolerance, and are therefore particularly vulnerable to extinction. We hypothesised that tolerance to multiple extreme conditions (e.g. low pH, hypoxia and drought) in brown mudfish Neochanna apoda, would increase their realised niche breadth because each extreme would provide additive refuge against a dominant species, the banded kokopu Galaxias fasciatus. Fish distributions were surveyed in 65 peat‐swamp‐forest streams and pools in New Zealand, which varied in dissolved oxygen, acidity and hydroperiod. Mudfish distribution was extremely patchy, and almost completely allopatric with kokopu. Allopatry was driven mainly by pool hydroperiod; mudfish occupied 88 percent of temporary pools due to their tolerance of habitat drying, whereas kokopu were absent from temporary pools. Within permanent pools, mudfish occurrence was negatively related to pool oxygen and pH, whereas kokopu occurrence was positively related to these conditions. Pool conditions were independently distributed in the landscape, suggesting that each abiotic stressor offered additive refuge for mudfish from kokopu predation/competition. Consequently, the mudfish realised niche breadth depended on the number of abiotic factors driving their allopatry with kokopu. Given the widespread negative relationships between niche breadth and species extinction probabilities, our results indicate that tolerance to multiple stressors may play an important role in insuring species persistence against the multiple drivers of global environmental change.
A framework for evaluating the influence of climate, dispersal limitation, and biotic interactions using fossil pollen associations across the late Quaternary
Authors: Blois Jessica L. , Gotelli Nicholas J. , Behrensmeyer Anna K. , Faith J. Tyler , Lyons S. Kathleen , Williams John W. , Amatangelo Kathryn L. , Bercovici Antoine , Du Andrew , Eronen Jussi T. , Graves Gary R. , Jud Nathan , Labandeira Conrad , Looy Cindy V. , McGill Brian , Patterson David , Potts Richard , Riddle Brett , Terry Rebecca , Tóth Anikó , Villaseñor Amelia , Wing Scott
Published: July 2014

Environmental conditions, dispersal lags, and interactions among species are major factors structuring communities through time and across space. Ecologists have emphasized the importance of biotic interactions in determining local patterns of species association. In contrast, abiotic limits, dispersal limitation, and historical factors have commonly been invoked to explain community structure patterns at larger spatiotemporal scales, such as the appearance of late Pleistocene no‐analog communities or latitudinal gradients of species richness in both modern and fossil assemblages. Quantifying the relative influence of these processes on species co‐occurrence patterns is not straightforward. We provide a framework for assessing causes of species associations by combining a null‐model analysis of co‐occurrence with additional analyses of climatic differences and spatial pattern for pairs of pollen taxa that are significantly associated across geographic space.

We tested this framework with data on associations among 106 fossil pollen taxa and paleoclimate simulations from eastern North America across the late Quaternary. The number and proportion of significantly associated taxon pairs increased over time, but only 449 of 56 194 taxon pairs were significantly different from random. Within this significant subset of pollen taxa, biotic interactions were rarely the exclusive cause of associations. Instead, climatic or spatial differences among sites were most frequently associated with significant patterns of taxon association. Most taxon pairs that exhibited co‐occurrence patterns indicative of biotic interactions at one time did not exhibit significant associations at other times. Evidence for environmental filtering and dispersal limitation was weakest for aggregated pairs between 16 and 11 kyr BP, suggesting enhanced importance of positive species interactions during this interval. The framework can thus be used to identify species associations that may reflect biotic interactions because these associations are not tied to environmental or spatial differences. Furthermore, temporally repeated analyses of spatial associations can reveal whether such associations persist through time.
MDPtoolbox: a multi‐platform toolbox to solve stochastic dynamic programming problems
Authors: Chadès Iadine , Chapron Guillaume , Cros Marie‐Josée , Garcia Frédérick , Sabbadin Régis
Published: July 2014

Stochastic dynamic programming (SDP) or Markov decision processes (MDP) are increasingly being used in ecology to find the best decisions over time and under uncertainty so that the chance of achieving an objective is maximised. To date, few programs are available to solve SDP/MDP. We present MDPtoolbox, a multi‐platform set of functions to solve Markov decision problems (MATLAB, GNU Octave, Scilab and R). MDPtoolbox provides state‐of‐the‐art and ready to use algorithms to solve a wide range of MDPs. MDPtoolbox is easy to use, freely available and has been continuously improved since 2004. We illustrate how to use MDPtoolbox on a dynamic reserve design problem.
Determinism of bacterial metacommunity dynamics in the southern East China Sea varies depending on hydrography
Authors: Yeh Yi‐Chun , Peres‐Neto Pedro R. , Huang Shiao‐Wei , Lai Yung‐Chih , Tu Chen‐Yi , Shiah Fuh‐Kwo , Gong Gwo‐Ching , Hsieh Chih‐hao
Published: July 2014

Spatial variation of communities composition (metacommunities) results from multiple assembly mechanisms, including environmental filtering and dispersal; however, whether and why the relative importance of the assembly mechanisms in shaping bacterial metacommunity changes through time in marine pelagic systems remains poorly studied. Here, we applied the elements of metacommunity structure framework and the variation partitioning framework to examine whether temporal variation of hydrographic conditions influences bacterioplankton metacommunity dynamics in the southern East China Sea (ECS). The spatiotemporal variation of bacterial communities composition was revealed using 454 pyrosequencing of 16S rDNA. In addition to the whole bacterial community, we analyzed four dominant taxonomic groups (Cyanobacteria, Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria) separately. Our analyses indicate that, considering the whole community level, the determinism of metacommunity structure varied among seasons. When the degree of connectivity was low (December), the metacommunity exhibited random distribution and was explained mainly by the environmental component. However, Clementsian metacommunity was found at intermediate connectivity (May), during which the environmental and spatial predictors were both significant. When connectivity was high (August), a random distribution pattern was found and no significant effect of environmental filtering or dispersal limitation was detected. Nevertheless, when considering different taxonomic groups, the differences in metacommunity dynamics among groups were found. Our results suggest that the driving forces of metacommunity dynamics varied depending on hydrography, as the degrees of environmental heterogeneity and connectivity among habitat patches were determined by circulation pattern. Moreover, mechanisms varied among different taxonomic groups, suggesting that differential dispersal capacity among taxonomic groups should be integrated into community assembly studies.
Mechanistic modelling of animal dispersal offers new insights into range expansion dynamics across fragmented landscapes
Authors: Bocedi Greta , Zurell Damaris , Reineking Björn , Travis Justin M. J.
Published: July 2014

Understanding and predicting the dynamics of range expansion is a major topic in ecology both for invasive species extending their ranges into non‐native regions and for species shifting their natural distributions as a consequence of climate change. In an increasingly modified landscape, a key question is ‘how do populations spread across patchy landscapes?‘ Dispersal is a central process in range expansion and while there is a considerable theory on how the shape of a dispersal kernel influences the rate of spread, we know much less about the relationships between emigration, movement and settlement rules, and invasion rates. Here, we use a simple, single species individual‐based model that explicitly simulates animal dispersal to establish how density‐dependent emigration and settlement rules interact with landscape characteristics to determine spread rates. We show that depending on the dispersal behaviour and on the risk of mortality in the matrix, increasing the number of patches does not necessarily maximise the spread rate. This is due to two effects: first, individuals dispersing at the expanding front are likely to exhibit lower net‐displacement as they typically do not travel far before finding a patch; secondly, with increasing availability of high quality habitat, density‐dependence in emigration and settlement can decrease the number of emigrants and their net‐displacement. The rate of spread is ultimately determined by the balance between net travelled distance, the dispersal mortality and the number of dispersing individuals, which in turn depend on the interaction between the landscape and the species’ dispersal behaviour. These results highlight that predicting spread rates in heterogeneous landscapes is a complex task and requires better understanding of the rules that individuals use in emigration, transfer and settlement decisions.
Herbivorous insect decreases plant nutrient uptake: the role of soil nutrient availability and association of below‐ground symbionts
Authors: KATAYAMA NOBORU , SILVA ALESSANDRO O. , KISHIDA OSAMU , USHIO MASAYUKI , KITA SATOSHI , OHGUSHI TAKAYUKI
Published: July 2014

1. Plants take nutrients from the rhizosphere via two pathways: (i) by absorbing soil nutrients directly via their roots and (ii) indirectly via symbiotic associations with nutrient‐providing microbes. Herbivorous insects can alter these pathways by herbivory, adding their excrement to the soil, and affecting plant–microbe associations.

2. Little is known, however, about the effects of herbivorous insects on plant nutrient uptake. Greenhouse experiments with soybean, aphids, and rhizobia were carried out to examine the effects of aphids on plant nutrient uptake.

3. First, the inorganic soil nitrogen and the sugar in aphid honeydew between aphid‐infected and ‐free plants were compared. It was found that aphid honeydew added 41 g m−2 of sugar to the soil, and that aphids decreased the inorganic soil nitrogen by 86%. This decrease may have been caused by microbial immobilisation of soil nitrogen followed by increased microbial abundance as a result of aphid honeydew.

4. Second, nitrogen forms in xylem sap between aphid‐infected and ‐free plants were compared to examine nitrogen uptake. Aphids decreased the nitrogen uptake via both pathways, and strength of the impact on direct uptake via plant roots was greater than indirect uptake via rhizobia. The reduced nitrogen uptake by the direct pathway was as a result of microbial immobilisation, and that by the indirect pathway was probably because of the interaction of microbial immobilisation and carbon stress, which was caused by aphid infection.

5. The present results demonstrate that herbivorous insects can negatively influence the two pathways of plant nutrient uptake and alter their relative importance.