bluuebunny/crossref_metadata_2025_split huggingface dataset:
Absorption profile and femtosecond intraband relaxation of the intense upper Davydov component in oligothiophenes
Authors: Petelenz Piotr , Kulig Waldemar 
Published: November 2010

AbstractThe diffuse shape of the high‐energy absorption band observed in oligothiophene crystals is interpreted in terms of Fano‐type mixing between the discrete upper Davydov component at k = 0 and the continuum of phonon‐accompanied exciton states at other values of crystal momentum. In temporal domain, this mixing is viewed as a crystal version of radiationless transition, and is followed by subsequent intra‐band exciton relaxation due to scattering processes with phonon release. The rates of energy dissipation in these latter processes, mediated by different intramolecular vibrational modes, are estimated from a simple expression based on the Fermi golden rule. Depopulation of long‐lived vibronic intermediates, acting as bottlenecks, is attributed to thermally activated processes with absorption of low‐frequency phonons. All essential input parameters are obtained from independent nonempirical calculations. The results are in excellent agreement both with the experimentally observed absorption band shapes and with energy‐dependent femtosecond dynamics afforded by measurements of sexithiophene (6T) fluorescence and photoinduced absorption.
Study on electrical properties of Si quantum dots based materials
Authors: Lin Dong , Ma Linzhi , Conibeer Gavin , Perez‐Wurfl Ivan 
Published: November 2010

AbstractThis article analyses silicon quantum dots based materials which could be used in all‐silicon tandem solar cells. The contact properties of aluminium and nickel on this material are obtained by circular transmission line measurements (TLM). Both metals make ohmic contacts with the material and the contact resistance is also similar for both metals, indicating that either the material is very heavily doped or the surface defect density is very high. Doping by diffusion is demonstrated for the first time on this material and a MOS structure is fabricated in order to extract doping type, doping concentration and mobility. A simple model is established for the MOS structure. Using capacitance versus voltage (C–V) measurements, we are able to extract doping concentration, mobility and surface charge by curve fitting. Using this fitting method, the relative permittivity of our material is estimated and an effective gate contact area is calculated for different frequencies, doping types and gate voltages. The doping concentration extracted is in the order of 1017 cm−3 and the mobility is two to three orders of magnitude lower compared to that of crystalline silicon with a similar doping level. Based on the C–V curves we can demonstrate that B behaves like a p‐type dopant and P as an n‐type dopant in our material.
Culture and Community Psychology: Toward a Renewed and Reimagined Vision
Authors: Kral Michael J. , Ramírez García Jorge I. , Aber Mark S. , Masood Nausheen , Dutta Urmitapa , Todd Nathan R. 
Published: November 2010

AbstractInterest is growing in community psychology to look more closely at culture. Culture has resided in community psychology in its emphasis on context, ecology, and diversity, however we believe that the field will benefit from a more explicit focus on culture. We suggest a cultural approach that values the community's points of view and an understanding of shared and divergent meanings, goals, and norms within a theory of empowerment. Furthermore, we posit the importance of pluralistic, multi‐method programs of research and action encompassing both idiographic and nomothetic approaches, and critical reflexivity of our roles and agendas. Culture can be further incorporated into all the branches and fibers of community psychology.
Managing Underwriters and the Marketing of Seasoned Equity Offerings
Authors: Huang Rongbing , Zhang Donghang 
Published: November 2010

AbstractUsing a sample of 2,281 seasoned equity offerings (SEOs) from 1995 to 2004, we show that the marketing of securities is important to issuers. The number of managing underwriters for an SEO is negatively related to the offer price discount, especially when the relative offer size is large and the stock return volatility is high. Larger investor networks of comanaging underwriters also lower offer price discounts. We argue that the evidence is supportive of the marketing hypothesis: The underwriters’ marketing efforts can lower the offer price discount by shifting up and flattening the demand curve of an SEO.
Point prevalence of bovine fascioliasis and the influence of chemotherapy on the milk yield in a lactating bovine population from the district of Toba Tek Singh, Pakistan
Authors: Khan M.K. , Sajid M.S. , Khan M.N. , Iqbal Z. , Arshad M. , Hussain A. 
Published: November 2010

AbstractThis paper provides an estimation of the point prevalence of fascioliasis and its economic impact in terms of increased milk yield after chemotherapy of a bovine population from the district of Toba Tek Singh, Punjab, Pakistan. A total of 2400 cattle and buffaloes were examined quantitatively using the McMaster egg-counting technique. Infected cattle and buffaloes (50 of each) were randomly selected and each divided into two groups of 25 animals. Groups A (buffaloes) and C (cattle) were treated with oxyclozanide (orally, 16.6 mg kg− 1body weight). Groups B and D served as negative controls for buffaloes and cattle, respectively. Pre- and post-treatment milk yield was recorded to determine if there were any changes in milk yield after treatment. Of 2400 faecal samples analysed, 654 (27.25%) were positive forFasciolaspp. with a mean number of eggs per gram (EPG) of 503.2. The point prevalence and worm burden of fascioliasis was significantly higher (OR = 2.13;P < 0.05) in buffaloes (34.58%; 415/1200; mean EPG maximum likelihood = 521.4) as compared to that of cattle (19.92%; 239/1200; mean EPG maximum likelihood = 415.8). Among the parasite species,F. gigantica(19.88%; 477/2400) was predominant (OR = 3.12;P < 0.05) as compared toF. hepatica(7.38%; 177/2400). An average daily increase of 0.67 and 0.87 litres of milk, with 0.41% and 0.37% more fat per animal, was observed in oxyclozanide-treated buffaloes and cattle, respectively. The economic value of reduced production of infected animals was estimated as US$0.33 and 0.32 per animal per day for cattle and buffaloes, respectively.
Verb argument structure acquisition in young children: defining a role for discourse
Authors: NAIGLES LETITIA R. , MALTEMPO ASHLEY 
Published: November 2010

ABSTRACTTwo-, three- and four-year-old English learners enacted sentences that were missing a direct object (e.g. *The zebra brings.). Previous work has indicated that preschoolers faced with such ungrammatical sentences consistently alter the usual meaning of the verb to fit the syntactic frame (enacting ‘zebra comes’); older children are more likely to repair the syntax to fit the meaning of the verb (enacting ‘zebra brings something’; Naigles, Gleitman & Gleitman, 1993). We investigated whether young children performed more repairs if an informative context preceded the ungrammatical sentences. Test sentences were preceded by short vignettes that created a relationship between three characters. Children repaired more sentences than had been found previously; however, older preschoolers also repaired significantly more frequently than younger preschoolers. Discourse context thus seems relevant to the acquisition of verb argument structure, but is not the sole source of information.
Predicting patterns of stress and mortality in intertidal invertebrates: applications of biophysical ecology in a changing world
Authors: Helmuth Brian , Kearney Michael , Sará Gianluca 
Published: November 2010

Abstract
Background
, Questions and Methods Recent studies have emphasized that local and geographic patterns of species distributions can be set by a variety of factors related to weather and climate, including exposure to lethal environmental conditions, indirect effects on consumers and competitors, and sublethal effects of physiological stress on growth and reproduction. Predicting where, when and with what magnitude these impacts are most (and least) likely to occur is imperative if we are to effectively plan for (i.e. adapt to) the effects of climate change.We developed a series of methods for translating patterns of environmental “signals” into organismal responses in intertidal ecosystems. Importantly, “organismal climatologies” – long term patterns of organism temperature measured using in situ biomimetic sensors - show distinct differences from patterns based on environmental temperature (air or water temperature). Similarly, we explored the use of dynamic energy budget models, linked to heat budget models of animal temperature, to examine temporal and spatial patterns of sublethal stress and growth.

Results and Conclusions
Comparisons of four different metrics of stress- seasonal averages, extreme temperatures, number of “stressful days” (>32°C) and return time of stress events – show that temporal and spatial patterns of sublethal stress do not always track patterns of lethal exposure. In other words, simply knowing average temperature often tells us very little about exposure to extremes and vice versa. These results are consistent with the idea that extreme events can occur during the temporal synchrony of multiple “normal” events- for example low wave splash, extreme low tides and high solar radiation. Results also suggest that the combination of heat budget models with dynamic energy budgets are potentially an effective way to predict spatial patterns of intertidal organisms, but that we still need more physiological data regarding the role of aerial body temperature in driving growth and reproduction.
Ontology--based Tools to Enhance the Curation Workflow
Authors: Whetzel Trish 
Published: November 2010

AbstractIn order to effectively search, retrieve, and analyze data oftentimes it is curated and tagged with ontology terms. However, the amount of effort to curate the existing set of data resources is beyond the limits of purely manual curation. We present three ontology-based tools developed by the National Center for Biomedical Ontology to enhance the curation workflow: Ontology Widgets, Notes, and the Annotator. The Ontology Widgets provide a mechanism to use ontologies in Web-based forms without the need to locally parse and store the ontology. The widgets provide a variety of functionality including term autocompletion and ontology visualization. The Ontology Widgets are implemented for all BioPortal ontologies, including those from the OBO Foundry and Unified Medical Language System. The Notes feature of BioPortal allows structured term proposals to be submitted in order to request the addition or modification of a term in an ontology. The term proposals can be added directly via the BioPortal Web interface or programmatically via the Notes Web service. Notification of new Notes and replies are both RSS- and Email-enabled. Once the term curation process is complete, the OWL class or OBO stanza can be generated via the Notes Web service. Finally, the Annotator can be used to automatically process textual metadata to identify ontology terms found within the text. The Annotator can be accessed programmatically via the Annotator Web service and can be used with all BioPortal ontologies. In summary, the Ontology Widgets, Notes, and Annotator provide mechanisms to enhance curation by helping collect annotated data upon data submission, by facilitating ontology term curation, and by tagging unstructured textual data with ontology terms.
Assessing the conservation value of farmland ponds: Use of predictive techniques to identify surrogare groups
Authors: Gioria Margherita 
Published: November 2010

Abstract
Background/Question/Methods.
Ponds are among the most diverse and yet threatened components of freshwater biodiversity. The conservation of ponds would greatly benefit from the identification of surrogate taxa in preliminary assessments aimed at detecting ponds of potentially high biodiversity value. Vascular plants and water beetles have often been used in pond conservation assessments. To evaluate whether wetland plants are a suitable surrogate group to evaluate pond biodiversity, we used plant, beetle, and environmental data collected from 54 ponds located in two farmed regions in Ireland. Specifically, we aimed at assessing cross-taxon congruence between water beetles and plants; quantifying and comparing the capacity of vegetation data and environmental variables to predict beetle species composition; assessing and comparing the response of plant and beetle communities to environmental conditions. The predictive strength of vegetation data was evaluated at the levels of species and community type composition, and species diversity. To identify the best predictor data-set for beetle species composition, we used predictive co-correspondence analysis (Co-CA) and predictive canonical correspondence analysis (CCA-PLS). Congruence in species richness was calculated using simple regression analysis, while a generalized linear model was developed to quantify the effect of environmental variables on patterns of beetle and plant diversity.

Results/Conclusions.
The study ponds supported over 30% of the Irish water beetle fauna (76 species), with five species having some form of IUCN Red List Status in Ireland, and 67 wetland plant species, including a nationally rare one. Co-CA showed that plant species composition had a positive predictive accuracy, which was significantly higher compared to that of data at the plant community type level. Although environmental variables showed a higher predictive capacity compared to that of plant species composition, the difference was not significant. Explanatory CCA analyses showed that plants and beetles both responded to the same subset of environmental conditions, explaining ca.18% of the variation in both plant and beetle species composition. Regional differences, permanency, substratum, and grazing intensity affected the composition of both plant and beetle assemblages. The relationship between plant and beetle diversity was rather weak, reflecting the contribution of few plant species in supporting diverse beetle assemblages. These findings have important implications in conservation planning. First, the composition of wetland plants can be effectively used as a surrogate taxon in the identification of conservation-priority ponds. Second, conservation strategies aimed at maintaining and enhancing pond biodiversity should be based on considerations on the vegetation.
The direct and indirect effects of the red imported fire ant (Solenopsis invicta) on seed fate in the longleaf pine ecosystem
Authors: Shearin Margaret , Kirkman L , Carroll Ronald 
Published: November 2010

AbstractInvasion of non-native ants potentially disrupts natural relationships of native ants and ant-dispersed plants. These relationships may be affected directly through seed collection, or indirectly though impacts on the native ant community. Solenopsis invicta (the red imported fire ant), a widespread invasive of the southeastern United States, negatively impacts human health, agriculture, and wildlife. The impacts of S. invicta on native plant communities are less understood, partially because the invasions are usually coupled with human disturbance of soil or vegetation. The longleaf pine ecosystem is one of the few native communities successfully invaded by S. invicta. In a natural stand of longleaf pine with native groundcover we determined the fate of seeds collected by S. invicta, and the change in the ant community and seed removal due to disturbance by timber harvesting activities. We used cafeteria-selection trials with seeds of native plants to determine rates of seed removal. We presented S. invicta with dyed elaiosome-bearing seeds and recovered seed in middens above ground, and we sampled nests below ground with a wax cast. To examine changes in the ant community following disturbance, we sampled the ant community before and after timber harvest using pitfall traps and observing seed removal.We found that S. invicta preferentially collects myrmecochorous (elaiosome-bearing) seeds. We recovered approximately 30 percent of the dyed seed on the surface in midden piles of which only 17 percent had elaiosomes removed. However, this response varies seasonally. No seeds were recovered in the fall, suggesting that S. invicta is either consuming or storing more seeds prior to cold weather. We recovered few seeds in the nest castes. Initial ant community composition sampling resulted in 24 species. S. invicta was strongly dominant in most plots, and removed 83% of all seeds taken by ants.
Pre and post fire carbon dynamics in a Florida Scrub oak
Authors: Bracho Rosvel , Thomas Cassondra , Li Jiahong , Powell Thomas , Hinkle C. Ross 
Published: November 2010

AbstractScrub oak is a xeromorphic shrub ecosystem discontinuously distributed in coastal and inland Florida. It supports a high biodiversity which includes a large number of endangered and threatened species. Its structural features are maintained by a fire return cycle of 7 to 10 years which maintains the biodiversity. Management of fire prone ecosystems such as this raises the question of whether the management strategy contributes to the system being a carbon sink or carbon source over the long-term. We used eddy covariance and biometric approaches to measure carbon dynamics in a Florida scrub oak ecosystem located at Kennedy Space Center in east Central Florida from April 2004 to December 2007. The study site was controlled burned in February 2006. Two years previous to fire, the site experienced average precipitation but drought conditions during the two years after fire. Net ecosystem production (NEP) was 419 g C m-2 yr-1 during the first year of measurements, and the ecosystem incorporated 823 g C m-2 during the 22 months before the fire. Aboveground net primary production (NPP) represented 50% of annual NEP. Carbon released by fire reached 316 g C m-2. Ecosystem respiration (Re) dominated the carbon balance during the first six months after fire, and the ecosystem released an extra 119 g C m-2. However, gross ecosystem production (GEP) increased with leaf area index (LAI) after fire, dominating the carbon balance during the following six months. The ecosystem was a carbon sink of 88 g C m-2 yr-1 during the first year after the fire. Leaf area index (LAI) reached 1.54 m2 m-2 by October 2007 (80% of pre-burn value for the same time period). The scrub oak ecosystem was a continuous carbon sink six months after the fire despite the dominant drought conditions during 2006 – 2007. The ecosystem offset 80% (251 g C m-2) of the carbon released in the fire during the following twenty two months after the fire. Considering the fire return cycle of 7 to 10 years and the fact that the study site and a similar site nearby incorporated more than 400 g C m-2 yr-1 during the two years before fire, this scrub oak is a net carbon sink in the landscape under current management strategies.
A hybrid approach to extract protein–protein interactions
Authors: Bui Quoc-Chinh , Katrenko Sophia , Sloot Peter M. A. 
Published: November 2010

Abstract
Motivation: Protein–protein interactions (PPIs) play an important role in understanding biological processes. Although recent research in text mining has achieved a significant progress in automatic PPI extraction from literature, performance of existing systems still needs to be improved.
Results: In this study, we propose a novel algorithm for extracting PPIs from literature which consists of two phases. First, we automatically categorize the data into subsets based on its semantic properties and extract candidate PPI pairs from these subsets. Second, we apply support vector machines (SVMs) to classify candidate PPI pairs using features specific for each subset. We obtain promising results on five benchmark datasets: AIMed, BioInfer, HPRD50, IEPA and LLL with F-scores ranging from 60% to 84%, which are comparable with the state-of-the-art PPI extraction systems. Furthermore, our system achieves the best performance on cross-corpora evaluation and comparative performance in terms of computational efficiency.
Availability: The source code and scripts used in this article are available for academic use at http://staff.science.uva.nl/~bui/PPIs.zip
Contact: bqchinh@gmail.com
Time of day influences cytokine and clock gene response to immune stimulation in equine whole blood
Authors: McGlynn O. F. , Browne J. A. , Blake C. M. , Murphy B. A. 
Published: November 2010

SummaryThe immune system demonstrates regularly recurring rhythmic variation that has important medical and veterinary clinical implications. Emerging evidence supports the existence of a bidirectional immune–circadian relationship during homeostatic challenge. In peripheral blood, circadian rhythmicity manifests in terms of clock gene expression, circulating levels and function of leucocyte cell populations and cytokine production. The involvement of interleukin 6 (IL6) in the transition from innate to acquired immunity is known, and inflammatory mediators can, in turn, phase shift peripheral molecular clocks. This study provides an initial investigation of diurnal variation in circadian clock and immune mediator response to antigenic challenge in the horse. Blood samples were collected at 4‐h intervals at circadian times (CT) 0, 4, 8, 12, 16 and 20 from healthy Thoroughbred fillies maintained under winter photoperiod. Heparinized blood was cultured at 37 °C for 6 h with or without lipolysaccharide (LPS) (1 μg/ml). Cells were harvested by the addition of PAXgene™ RNA stabilizer solution to immediately preserve the RNA profile. Analyses of Taqman qPCR expression data reveal a significant CT X LPS interaction for the canonical clock genes PER2, CRY1, ARNTL, NR1D2 (P < 0.001, P < 0.05, P < 0.05, P < 0.01 respectively) and the immunomodulatory cytokine IL6 (P < 0.0001). LPS upregulated IL1B levels (P < 0.01), but there was no effect of CT. These results confirm that peripheral blood differentially responds to antigenic challenge over the 24‐h cycle, impacting on our understanding of the pathophysiology of inflammatory responses. Further research in this area should provide valuable information regarding the optimum time for drug delivery and vaccination.
Comparative human–horse sequence analysis of theCYP3Asubfamily gene cluster
Authors: Schmitz A. , Demmel S. , Peters L. M. , Leeb T. , Mevissen M. , Haase B. 
Published: November 2010

SummaryCytochrome P450 enzymes (CYP450s) represent a superfamily of haem–thiolate proteins. CYP450s are most abundant in the liver, a major site of drug metabolism, and play key roles in the metabolism of a variety of substrates, including drugs and environmental contaminants. Interaction of two or more different drugs with the same enzyme can account for adverse effects and failure of therapy. Human CYP3A4 metabolizes about 50% of all known drugs, but little is known about the orthologous CYP450s in horses. We report here the genomic organization of the equineCYP3Agene cluster as well as a comparative analysis with the humanCYP3Agene cluster. The equineCYP450genes of the3Afamily are located on ECA 13 between 6.97–7.53 Mb, in a region syntenic to HSA 7 99.05–99.35 Mb. Seven potential, closely linked equineCYP3Agenes were found, in contrast to only four genes in the human genome. RNA was isolated from an equine liver sample, and the approximately 1.5‐ kb coding sequence of sixCYP3Agenes could be amplified by RT‐PCR. Sequencing of the RT‐PCR products revealed numerous hitherto unknown single nucleotide polymorphisms (SNPs) in these sixCYP3Agenes, and one 6‐ bp deletion compared to the reference sequence (EquCab2.0). The presence of the variants was confirmed in a sample of genomic DNA from the same horse. In conclusion, orthologous genes for theCYP3Afamily exist in horses, but their number differs from those of the humanCYP3Agene family.CYP450genes of the same family show high homology within and between mammalian species, but can be highly polymorphic.