bluuebunny/crossref_metadata_2025_split huggingface dataset:
Invasive Plant (Microstegium vimineum) Reduces Abundance and Richness of Insect Communities
Authors: Simao Maria Carolina , Rudgers Jennifer , Flory S. Luke 
Published: August 2009

AbstractPlant invasions are known to have negative impacts on native plant communities, yet their effects on higher trophic levels have not been well documented. Past studies investigating the effects of invasive plants on herbivores and carnivores have been largely observational in nature and thus lack the ability to tease apart whether differences are a cause or consequence of the invasion. In addition, understanding how plant traits and plant species compositions change in invaded habitats may increase our ability to predict when and where invasive plants will have effects that cascade to animals. We experimentally introduced a non-native plant (Microstegium vimineum, Japanese stiltgrass) to evaluate impacts on arthropods. We also investigated possible mechanisms through which the invader could affect associated arthropods, including changes in native plant species richness, aboveground plant biomass, light availability, and vegetation height. In experimentally invaded plots, arthropod abundance was reduced by 39%, and species richness declined by 19%. Carnivores experienced greater reductions in abundance than herbivores (61% versus 31% reduction). Arthropod composition significantly diverged between experimentally invaded and control plots, and particular species belonging to the families Aphididae (aphids), Formicidae (ants) and Phalacridae (shining flower beetles) contributed the most to compositional differences. Among the mechanisms we investigated, only the reduction in native plant species richness caused by invasion was strongly correlated with total arthropod abundance and richness. In sum, our results demonstrate negative impacts of M. vimineum invasion on higher trophic levels and suggest that these effects occur, in part, indirectly through invader-mediated reductions in the richness of the native plant community. The particularly strong response of carnivores suggests that plant invasion could reduce top-down control of herbivorous species for native plants. The cascading effects of plant invasion on arthropods reported here reinforce motivation to control M. vimineum spread.
Changes in Simpson’s Diversity Index in Microcosms Impacted with Monosodium Methane Arsenate
Authors: Kish Peter , Daniel Nelson 
Published: August 2009

AbstractThe objective of our studies is to analyze environmental impacts of Monosodium Methane Arsenate, MSMA, on aquatic habitats using the Aqua-Terra microcosm system. MSMA was applied at environmentally relevant(recommended) doses to microcosms to determine the change in biodiversity and the bio-concentration of arsenic in the aquatic plants (Elodea Sp.) used in the microcosms as an oxygen source. The microcosms are filled with unfiltered pond water and the diversity of each microcosm was determined before application of the herbicide. After population stabilization, the herbicide is applied to the terrestrial portion of the microcosm. The herbicide is watered into the microcosm by allowing the herbicide to be filtered by soil into the aquatic portion of the microcosm. Diversity of the microcosm was determined by physical counts of invertebrate organisms and quantified using Simpson’s Index of Diversity. Calculating Simpson’s Index of Diversity indicate there is an overall decline in the diversity of the microcosms from 0.327 to 0.763 for recommended manufacturer’s formulation and 0.512 to 0.546 for twice the recommended manufacturer’s formulation. Plants take up arsenic using the same metabolic pathways that they use to take up phosphorus. This makes arsenic available for trophic transfer to the primary consumers as any primary producer is consumed. In Elodea sp., total arsenic concentrations (ashed from fresh samples) range from 15 ppb to 214 ppb before and after application of the herbicide. Water samples show the same increase, from 5 ppb to 70 ppb before and after application. These data indicate that the arsenic in the MSMA compound is either being liberated by bacterial decomposing or it is passing through the soil unmodified.
Five years of winter climate change-related research in the Canadian low Arctic: What have we learned?
Authors: Grogan Paul , Buckeridge Kate 
Published: August 2009

AbstractThe importance of the fall, winter and spring periods to ecosystem functioning and biogeochemical cycling in tundra has only become apparent in the past two decades. Our research group has been conducting winter climate change-related studies at a low arctic tundra site near Daring Lake, north of Yellowknife in northern Canada for the past five years. Most of these studies have focused on the biogeochemical interactions between plants, soils, and soil microbes during fall, winter and spring, and on their responses to experimentally deepened snow. In addition, we have measured trace gas production and isotopic nitrogen tracer distributions among plant and soil components in several vegetation-types. The central goal has been to understand the potential importance of cold season soil N transformation processes to ecosystem-level biogeochemistry during the subsequent plant growing season, and then to develop predictions of how changes in winter climate may impact these seasonal processes. In this talk, I will present a synthesis of those studies, emphasizing temperature-moisture interactions, and highlighting future research priorities.
Local winter deer density: Effects of forest structure and snow in a managed forest landscape
Authors: Millington James , Walters Michael , Matonis Megan , Liu Jianguo 
Published: August 2009

Abstract
Background/Questions/Methods
White-tailed deer (Odocoileus virginianus) are a ‘keystone herbivore’ with the potential to cause tree regeneration failure and greatly affect vegetation dynamics, stand structure and ecological function of forests across eastern North America. In northern mixed conifer-hardwood forests, local winter-time deer populations are dependent on habitat characterized by patterns of forest cover that provide shelter from snow and cold temperatures (lowland conifer stands) in close proximity to winter food (deciduous hardwood stands). Stand structure may also influence winter spatial deer distribution. Consequently, modification of forest cover patterns and stand structure by timber harvesting will affect local spatial deer distributions, with potential ecological and economic consequences. Here, we ask if forest cover pattern and stand structure, and their interactions with snow depth, can explain winter deer density in the managed forests of the central Upper Peninsula of Michigan, USA. For each local winter deer density estimate (from fecal pellet counts) we calculate stand-level characteristics for surrounding ‘landscapes of influence’ of radius 200 m. For these data, and modeled snow depth estimates, we use multivariate techniques to produce predictive models and to identify the most important factors driving local deer densities across our 400,000 ha study area.

Results/Conclusions
Distance to the nearest conifer stand consistently explains the most variance in univariate regression models. Deer densities are highest near lowland conifer stands in areas where mean hardwood tree diameter-at-breast-height is low. Multiple regression models including these factors explain 22% of variance in deer density and have up to a 65% chance of correctly ranking a site’s deer density (relative to other sites within our study area). We use model ensembles to produce maps of estimated deer density (and associated uncertainty) for a subset of our study area and show how managers might use these maps to aid co-management of deer and forest regeneration. Our results highlight the importance of local and regional factors (forest cover-type pattern, stand structure, climate) on winter white-tailed deer density in managed hardwood-conifer forests. Use of these results, and the simulation model being developed, will help identify management practices that can decrease deer impacts and ensure the ecological and economic sustainability of forests in which deer browse is proving problematic for tree regeneration.
Producing American English Vowels During Vocal Tract Growth: A Perceptual Categorization Study of Synthesized Vowels
Authors: Ménard Lucie , Davis Barbara L. , Boë Louis-Jean , Roy Johanna-Pascale 
Published: August 2009

Purpose
To consider interactions of vocal tract change with growth and perceived output patterns across development, the influence of nonuniform vocal tract growth on the ability to reach acoustic–perceptual targets for English vowels was studied.

Method
Thirty-seven American English speakers participated in a perceptual categorization experiment. For the experiment, an articulatory-to-acoustic model was used to synthesize 342 five-formant vowels, covering maximal vowel spaces for speakers at 5 growth stages (from 6 months old to adult).

Results
Results indicate that the 3 vowels /i u æ/ can be correctly perceived by adult listeners when produced by speakers with a 6-month-old vocal tract. Articulatory-to-acoustic relationships for these 3 vowels differ across growth stages. For a given perceived vowel category, the infant’s tongue position is more fronted than the adult’s. Furthermore, nonuniform vocal tract growth influences degree of interarticulator coupling for a given perceived vowel, leading to a reduced correlation between jaw height and tongue body position in infantlike compared with adult vocal tracts.

Conclusion
Findings suggest that nonuniform vocal tract growth does not prevent the speaker from producing acoustic–auditory targets related to American English vowels. However, the relationships between articulatory configurations and perceptual targets change from birth to adulthood.
Liver vessel enhancement by gd-bopta and gd-eob-dtpa: a comparison in healthy volunteers
Authors: Brismar T. B. , Dahlström N. , Edsborg N. , Persson A. , Smedby Ö. , Albiin N. 
Published: August 2009

Background: A thorough understanding of magnetic resonance (MR) contrast media dynamics makes it possible to choose the optimal contrast media for each investigation. Differences in visualizing hepatobiliary function between Gd-BOPTA and Gd-EOB-DTPA have previously been demonstrated, but less has been published regarding differences in liver vessel visualization. Purpose: To compare the liver vessel and liver parenchymal enhancement dynamics of Gd-BOPTA (MultiHance) and Gd-EOB-DTPA (Primovist). Material and Methods: The signal intensity of the liver parenchyma, the common hepatic artery, the middle hepatic vein, and a segmental branch of the right portal vein was obtained in 10 healthy volunteers before contrast media administration, during arterial and portal venous phases, and 10, 20, 30, 40, and 130 min after intravenous contrast medium injection, but, due to scanner limitations, not during the hepatic venous phase. The doses of contrast media were 0.1 mmol/kg for Gd-BOPTA and 0.025 mmol/kg for Gd-EOB-DTPA. Results: Maximum enhancement of liver parenchyma was observed from the portal venous phase until 130 min after Gd-BOPTA administration and from 10 min to 40 min after Gd-EOB-DTPA. There was no difference in maximum enhancement of liver parenchyma between the two contrast media. When using Gd-BOPTA, the vascular contrast enhancement was still apparent 40 min after injection, but had vanished 10 min after Gd-EOB-DTPA injection. The maximum difference in signal intensity between the vessels and the liver parenchyma was significantly greater with Gd-BOPTA than with Gd-EOB-DTPA ( P<0.0001). Conclusion: At the dosage used in this study, Gd-BOPTA yields higher maximum enhancement of the hepatic artery, portal vein, and middle hepatic vein during the arterial and the portal venous phase and during the delayed phases than Gd-EOB-DTPA does, whereas there is no difference in liver parenchymal enhancement between the two contrast agents.
The Competitive Process in the Age of the Internet
Authors: Earl Peter E. , Mandeville Tom 
Published: August 2009

Abstract
This paper examines some of the impacts of the widespread adoption and use of the Internet in advanced countries on business, consumers and the media. It is argued that while capital costs of entry into Internet‐based businesses may be very low, this does not guarantee that markets in which such firms operate will necessarily be hotly contested, for success may require substantial sunk costs to be incurred in development. It explores the changing nature of market institutions associated with the rise of e‐commerce (including the advent of what are labelled ‘portal’ firms) and associated changes in the division of labour between buyers, sellers and intermediaries. The authors provide behavioural, evolutionary, and information theoretic perspectives on these dynamic issues.
Top‐Down e‐Infrastructure Meets Bottom‐Up Research Innovation: The Social Shaping of e‐Research
Authors: Meyer Eric T. , Dutton William H. 
Published: August 2009

Abstract
Are advances in ICTs enabling positive transformations in academic research practices? This paper explores key themes emerging from a 2008 survey of researchers aimed at identifying use and non‐use of advanced ICTs for research. Deterministic perspectives on e‐Research suggest that new e‐infrastructures will reshape research in predictable ways, such as by fostering more collaboration. In contrast, social shaping perspectives lead to the expectation that existing practices and institutions will shape the ways in which e‐Research is employed. This exploratory study found that individual variations across researchers cluster into identifiable groupings of research practices, which help to illuminate involvement in e‐Research, and differences in methods and research software used across the disciplines. In line with a social shaping perspective, the findings suggest that, in the social sciences, top‐down visions of e‐infrastructure development need to be tied to the realities of bottom‐up patterns of innovation in approaches to e‐Research.
A Socio‐cognitive Perspective of Industry Innovation Initiatives
Authors: Sneddon Joanne , Soutar Geoffrey , Mazzarol Tim 
Published: August 2009

Abstract
This article contributes to the emerging theory of industry belief systems and the social construction of innovation by examining how industry actors conceptualise and negotiate industry transformation through the development and diffusion of new technologies. In a qualitative study of innovation in the Australian wool industry, we found that the social construction of industry belief systems and new technologies was an evolutionary process of social sensemaking in which there was reciprocity between individual and collective meaning‐making that reflected conflict, consensus and compliance between industry actors about new technologies and industry beliefs.
Can Environmental Promotion Backfire? Evidence from the Vehicle Market
Authors: Teisl Mario F. , Noblet Caroline L. , Rubin Jonathan 
Published: August 2009

Several studies document the potential for eco-labeling and marketing programs; however, they focused on inexpensive, frequently purchased items. We identify whether such programs can be effective with more expensive, durable goods. We isolate the impact of the program on consumers by analyzing responses to a survey administered before and after the program to independent samples of individuals residing in and out of the marketing area. We used both multivariate analysis of variance and regression approaches in the analyses. Few vehicle dealers participated in the eco-labeling portion and we find the eco-marketing component of the program led to only one positive outcome; individuals exposed to the marketing are less likely to think all vehicles pollute about the same when driven. This was one of the key misperceptions that the Maine Clean Car Campaign attempted to correct. However, we also found three negative impacts of the Campaign. Individuals exposed to the marketing viewed vehicle emissions as being a smaller contributor to Maine's air quality problems and had an increased perception that greener vehicles suffered from poor performance and were more expensive. [Supplementary materials are available for this article. Go to the publisher's online edition of Social Marketing Quarterly for the following free supplemental resources: results of data analyses.]
A boosting approach to structure learning of graphs with and without prior knowledge
Authors: Anjum Shahzia , Doucet Arnaud , Holmes Chris C. 
Published: August 2009

AbstractMotivation: Identifying the network structure through which genes and their products interact can help to elucidate normal cell physiology as well as the genetic architecture of pathological phenotypes. Recently, a number of gene network inference tools have appeared based on Gaussian graphical model representations. Following this, we introduce a novel Boosting approach to learn the structure of a high-dimensional Gaussian graphical model motivated by the applications in genomics. A particular emphasis is paid to the inclusion of partial prior knowledge on the structure of the graph. With the increasing availability of pathway information and large-scale gene expression datasets, we believe that conditioning on prior knowledge will be an important aspect in raising the statistical power of structural learning algorithms to infer true conditional dependencies.Results: Our Boosting approach, termed BoostiGraph, is conceptually and algorithmically simple. It complements recent work on the network inference problem based on Lasso-type approaches. BoostiGraph is computationally cheap and is applicable to very high-dimensional graphs. For example, on graphs of order 5000 nodes, it is able to map out paths for the conditional independence structure in few minutes. Using computer simulations, we investigate the ability of our method with and without prior information to infer Gaussian graphical models from artificial as well as actual microarray datasets. The experimental results demonstrate that, using our method, it is possible to recover the true network topology with relatively high accuracy.Availability: This method and all other associated files are freely available from http://www.stats.ox.ac.uk/∼anjum/.Contact: s.anjum@har.mrc.ac.uk; cholmes@stats.ox.ac.ukSupplementary information: Supplementary data are available at Bioinfomatics online.
GRIMP: a web- and grid-based tool for high-speed analysis of large-scale genome-wide association using imputed data
Authors: Estrada Karol , Abuseiris Anis , Grosveld Frank G. , Uitterlinden André G. , Knoch Tobias A. , Rivadeneira Fernando 
Published: August 2009

Abstract
Summary: The current fast growth of genome-wide association studies (GWAS) combined with now common computationally expensive imputation requires the online access of large user groups to high-performance computing resources capable of analyzing rapidly and efficiently millions of genetic markers for ten thousands of individuals. Here, we present a web-based interface—called GRIMP—to run publicly available genetic software for extremely large GWAS on scalable super-computing grid infrastructures. This is of major importance for the enlargement of GWAS with the availability of whole-genome sequence data from the 1000 Genomes Project and for future whole-population efforts.
Contact: ta.knoch@taknoch.org; f.rivadeneira@erasmusmc.nl
Metabolite and reaction inference based on enzyme specificities
Authors: de Groot M. J. L. , van Berlo R. J. P. , van Winden W. A. , Verheijen P. J. T. , Reinders M. J. T. , de Ridder D. 
Published: August 2009

AbstractMotivation: Many enzymes are not absolutely specific, or even promiscuous: they can catalyze transformations of more compounds than the traditional ones as listed in, e.g. KEGG. This information is currently only available in databases, such as the BRENDA enzyme activity database. In this article, we propose to model enzyme aspecificity by predicting whether an input compound is likely to be transformed by a certain enzyme. Such a predictor has many applications, for example, to complete reconstructed metabolic networks, to aid in metabolic engineering or to help identify unknown peaks in mass spectra.Results: We have developed a system for metabolite and reaction inference based on enzyme specificities (MaRIboES). It employs structural and stereochemistry similarity measures and molecular fingerprints to generalize enzymatic reactions based on data available in BRENDA. Leave-one-out cross-validation shows that 80% of known reactions are predicted well. Application to the yeast glycolytic and pentose phosphate pathways predicts a large number of known and new reactions, often leading to the formation of novel compounds, as well as a number of interesting bypasses and cross-links.Availability: Matlab and C++ code is freely available at https://gforge.nbic.nl/projects/mariboes/Contact: d.deridder@tudelft.nlSupplementary information: Supplementary data are available at Bioinformatics online.
ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes
Authors: Kristiansson Erik , Hugenholtz Philip , Dalevi Daniel 
Published: August 2009

Abstract
Summary: Microorganisms are ubiquitous in nature and constitute intrinsic parts of almost every ecosystem. A culture-independent and powerful way to study microbial communities is metagenomics. In such studies, functional analysis is performed on fragmented genetic material from multiple species in the community. The recent advances in high-throughput sequencing have greatly increased the amount of data in metagenomic projects. At present, there is an urgent need for efficient statistical tools to analyse these data. We have created ShotgunFunctionalizeR, an R-package for functional comparison of metagenomes. The package contains tools for importing, annotating and visualizing metagenomic data produced by shotgun high-throughput sequencing. ShotgunFunctionalizeR contains several statistical procedures for assessing functional differences between samples, both for individual genes and for entire pathways. In addition to standard and previously published methods, we have developed and implemented a novel approach based on a Poisson model. This procedure is highly flexible and thus applicable to a wide range of different experimental designs. We demonstrate the potential of ShotgunFunctionalizeR by performing a regression analysis on metagenomes sampled at multiple depths in the Pacific Ocean.
Availability: http://shotgun.zool.gu.se
Contact: dalevi@chalmers.se; erik.kristiansson@zool.gu.se
Supplementary information: supplementary data are available at Bioinformatics online.
PiSQRD: a web server for decomposing proteins into quasi-rigid dynamical domains
Authors: Aleksiev T. , Potestio R. , Pontiggia F. , Cozzini S. , Micheletti C. 
Published: August 2009

Abstract
Summary: The PiSQRD web resource can be used to subdivide protein structures in quasi-rigid dynamical domains. The latter are groups of amino acids behaving as approximately rigid units in the course of protein equilibrium fluctuations. The PiSQRD server takes as input a biomolecular structure and the desired fraction of protein internal fluctuations that must be accounted for by the relative rigid-body motion of the dynamical domains. Next, the lowest energy modes of fluctuation of the protein (optionally provided by the user) are calculated and used to identify the rigid subunits. The resulting optimal subdivision is returned through a web page containing both interactive graphics and detailed data output.
Availability: The PiSQRD web server, which requires Java, is available free of charge for academic users at http://pisqrd.escience-lab.org.
Contact: potestio@sissa.it