bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parental crowding influences life-history traits inLocusta migratoriafemales
Authors: Chapuis M.-P. , Crespin L. , Estoup A. , Augé-Sabatier A. , Foucart A. , Lecoq M. , Michalakis Y. 
Published: May 2009

AbstractParental environments could play an important role in controlling insect outbreaks, provided they influence changes in physiological, developmental or behavioural life-history traits related to fluctuations in population density. However, the potential implication of parental influence in density-related changes in life-history traits remains unclear in many insects that exhibit fluctuating population dynamics, particularly locusts. In this study, we report a laboratory experiment, which enabled us to characterize the life-history trait modifications induced by parental crowding of female individuals from a frequently outbreaking population ofLocusta migratoria(Linnaeus) (Orthoptera: Acrididae). We found that a rearing history of crowding led to reduced female oviposition times and increased offspring size but did not affect the developmental time, survival, fecundity, and the sex-ratio and the number of offspring. Because all studied females were raised in a common environment (isolation conditions), these observed reproductive differences are due to trans-generational effects induced by density. We discuss the ecological and evolutionary implications of the observed density-dependent parental effects on the life-history ofL. migratoria.
Comparison of synthetic membranes in the development of anin vitrofeeding system forDermanyssus gallinae
Authors: Harrington D.W.J. , Guy J.H. , Robinson K. , Sparagano O.A.E. 
Published: May 2009

AbstractAlthough artificial feeding models for the poultry red mite (Dermanyssus gallinae) most frequently use biological membranes consisting of day-old chick skin, there are ethical considerations associated with the use of skin. The few studies reported in the literature that have investigated the use of synthetic membranes to feedD. gallinae in vitrohave reported limited success. The current study describes an investigation into the use of synthetic membranes made from either Nescofilm® or rayon and silicone, used either alone or in combination with different feather or skin extracts, as well as the use of capillary tubes. In all, 12 different treatments were used, and the feeding rate ofD. gallinaewas compared to that of day-old chick skin. Allowing mites to feed on a membrane consisting of Nescofilm with a skin extract resulted in the highest proportion of mites feeding (32.3%), which was not significantly different to the feeding rate of mites on day-old chick skin (38.8%). This study confirms that synthetic membranes can be used to feedD. gallinaeartificially. Further optimization of the membrane and mite storage conditions is still necessary, but the study demonstrates a proof of concept.
Distribution of mosquitoes in relation to urban landscape characteristics
Authors: Gleiser R.M. , Zalazar L.P. 
Published: May 2009

AbstractThe current global increase in prevalence of vector borne diseases, as well as an expansion of tropical infections to more temperate zones, justifies further studies on vector populations. Urban areas may favour viral transmission to humans through close contacts between the vectors and the vertebrate hosts, and also affecting mosquito populations by offering larval habitat, refuges and adequate microclimates to survive the winter. This work analyses the spatial distribution of potential vector mosquitoes in relation to landscape characteristics in an urban environment in a temperate climate region. Mosquitoes were trapped monthly from October 2005 to March 2006 in 25 sites within Córdoba city and suburbs with miniature light traps+CO2. Nine species were collected, and the most abundant were Culex quinquefasciatus (37.1%), C. apicinus (26.6%) and Aedes aegypti (13.9%). Species that may be involved in SLEv transmission were recorded throughout the sampling. C. quinquefasciatus was detected in 92% of the sites; however, only two sites showed consistently larger collections. The site of highest C. quinquefasciatus abundance was located within an area of high Saint Louis Encefalitis virus prevalence and risk of infection, further supporting this species involvement as a vector. Significant correlations were detected between land cover characteristics and abundance of C. apicinus, C. interfor and C. maxi that were consistent with previous knowledge about their larval habitat and domestic preferences, which may be useful for targeting vector control operations.
HOW CAN AGRICULTURE RESEARCH MAKE A DIFFERENCE IN COUNTRIES EMERGING FROM CONFLICT?
Authors: ERSKINE W. , NESBITT H. 
Published: May 2009

SUMMARYConflict is the most common cause of food insecurity. Foreign aid to countries emerging from conflict often allows a funded but brief window for the confirmation-testing and diffusion of agricultural innovation in affected areas. This paper asks the question: what lessons has agricultural research learned through its involvement in this process in countries emerging from conflict? Drawing on experience from Afghanistan and other countries, this paper documents some cases in which it has been possible to inject an element of simple hypothesis testing, often in farmer-managed trials, into post-conflict plans leading to useful lessons. Agricultural researchers need to be cognizant of this approach so that the practice becomes more widely used and lessons recorded for future use.
Does rational analysis stand up to rational analysis?
Authors: Evans Jonathan St. B. T. 
Published: May 2009

AbstractI agree with Oaksford & Chater (O&C) that human beings resemble Bayesian reasoners much more closely than ones engaging standard logic. However, I have many problems with their “rational analysis” framework, which appears to be rooted in normative rather than ecological rationality. The authors also overstate everyday rationality and neglect to account for much relevant psychological work on reasoning.
Design, analysis, and stiffness optimization of a three degree of freedom parallel manipulator
Authors: Gao Zhen , Zhang Dan , Hu Xiaolin , Ge Yunjian 
Published: May 2009

SUMMARYThis paper proposed a novel three degree of freedom (DOF) parallel manipulator—two translations and one rotation. The mobility study and inverse kinematic analysis are conducted, and a CAD model is presented showing the design features. The optimization techniques based on artificial intelligence approaches are investigated to improve the system stiffness of the proposed 3-DOF parallel manipulator. Genetic algorithms and artificial neural networks are implemented as the intelligent optimization methods for the stiffness synthesis. The mean value and the standard deviation of the global stiffness distribution are proposed as the design indices. Both the single objective and multi-objective optimization issues are addressed. The effectiveness of this methodology is validated with Matlab.
Smooth structures and Einstein metrics on
Authors: RǍSDEACONU RAREŞ , ŞUVAINA IOANA 
Published: May 2009

AbstractWe show that each of the topological 4-manifolds $\bcp^2\# k\overline{\bcp^2}$, for k = 5, 6, 7, 8 admits a smooth structure which has an Einstein metric of scalar curvature s > 0, a smooth structure which carries an Einstein metric with s < 0 and infinitely many non-diffeomorphic smooth structures which do not admit Einstein metrics. We also exhibit new examples of higher dimensional manifolds carrying Einstein metrics of both positive and negative scalar curvature.
Motivic integration and projective bundle theorem in morphic cohomology
Authors: TEH JYH-HAUR 
Published: May 2009

AbstractWe reformulate the construction of Kontsevich's completion and use Lawson homology to define many new motivic invariants. We show that the dimensions of subspaces generated by algebraic cycles of the cohomology groups of two K-equivalent varieties are the same, which implies that several conjectures of algebraic cycles are K-statements. We define stringy functions which enable us to ask stringy Grothendieck standard conjecture and stringy Hodge conjecture. We prove a projective bundle theorem in morphic cohomology for trivial bundles over any normal quasi-projective varieties.
Peas and pancakes: On apparent disagreement and (null) light verbs in Swedish
Authors: Josefsson Gunlög 
Published: May 2009

Two variants of what looks like disagreement between a subject and a predicative adjective are explored:(i)(ii)Having shown how Construction NOM and Construction PROP differ, I demonstrate that the subject of Construction PROP is clausal. I argue that the topmost XP of the subject phrase of both constructions contains a null neuter element. This accounts for the neuter predicative agreement; hence the idea of default agreement or semantic agreement can be dismissed. I also argue that the subject in (ii) contains avP, the head of which is a null light verb. Other instances of null light verbs in Swedish are identified too. Finally, I propose an analysis that accounts for the close relation between Construction PROP and the corresponding construction with amed-phrase ‘with-phrase’.
MetNetAligner: a web service tool for metabolic network alignments
Authors: Cheng Qiong , Harrison Robert , Zelikovsky Alexander 
Published: May 2009

Abstract
Summary: The accumulation of high-throughput genomic, proteomic and metabolical data allows for increasingly accurate modeling and reconstruction of metabolic networks. Alignment of the reconstructed networks can help to catch model inconsistencies and infer missing elements. In this note, we present the web service tool MetNetAligner which aligns metabolic networks, taking in account the similarity of network topology and the enzymes' functions. It can be used for predicting unknown pathways, comparing and finding conserved patterns and resolving ambiguous identification of enzymes. The tool supports several alignment options including allowing or forbidding enzyme deletion and insertion. It is based on a novel scoring scheme which measures enzyme-to-enzyme functional similarity and a fast algorithm which efficiently finds optimal mappings from a directed graph with restricted cyclic structure to an arbitrary directed graph.
Availability: MetNetAligner is available as web-server at: http://alla.cs.gsu.edu:8080/MinePW/pages/gmapping/GMMain.html.
Contact: alexz@cs.gsu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
A tool for identification of genes expressed in patterns of interest using the Allen Brain Atlas
Authors: Davis Fred P. , Eddy Sean R. 
Published: May 2009

Abstract
Motivation: Gene expression patterns can be useful in understanding the structural organization of the brain and the regulatory logic that governs its myriad cell types. A particularly rich source of spatial expression data is the Allen Brain Atlas (ABA), a comprehensive genome-wide in situ hybridization study of the adult mouse brain. Here, we present an open-source program, ALLENMINER, that searches the ABA for genes that are expressed, enriched, patterned or graded in a user-specified region of interest.
Results: Regionally enriched genes identified by ALLENMINER accurately reflect the in situ data (95–99% concordance with manual curation) and compare with regional microarray studies as expected from previous comparisons (61–80% concordance). We demonstrate the utility of ALLENMINER by identifying genes that exhibit patterned expression in the caudoputamen and neocortex. We discuss general characteristics of gene expression in the mouse brain and the potential application of ALLENMINER to design strategies for specific genetic access to brain regions and cell types.
Availability: ALLENMINER is freely available on the Internet at http://research.janelia.org/davis/allenminer.
Contact: davisf@janelia.hhmi.org
Supplementary information: Supplementary data are available at Bioinformatics online.
U-Compare: share and compare text mining tools with UIMA
Authors: Kano Yoshinobu , Baumgartner William A. , McCrohon Luke , Ananiadou Sophia , Cohen K. Bretonnel , Hunter Lawrence , Tsujii Jun'ichi 
Published: May 2009

Abstract
Summary: Due to the increasing number of text mining resources (tools and corpora) available to biologists, interoperability issues between these resources are becoming significant obstacles to using them effectively. UIMA, the Unstructured Information Management Architecture, is an open framework designed to aid in the construction of more interoperable tools. U-Compare is built on top of the UIMA framework, and provides both a concrete framework for out-of-the-box text mining and a sophisticated evaluation platform allowing users to run specific tools on any target text, generating both detailed statistics and instance-based visualizations of outputs. U-Compare is a joint project, providing the world's largest, and still growing, collection of UIMA-compatible resources. These resources, originally developed by different groups for a variety of domains, include many famous tools and corpora. U-Compare can be launched straight from the web, without needing to be manually installed. All U-Compare components are provided ready-to-use and can be combined easily via a drag-and-drop interface without any programming. External UIMA components can also simply be mixed with U-Compare components, without distinguishing between locally and remotely deployed resources.
Availability: http://u-compare.org/
Contact: kano@is.s.u-tokyo.ac.jp
apLCMS—adaptive processing of high-resolution LC/MS data
Authors: Yu Tianwei , Park Youngja , Johnson Jennifer M. , Jones Dean P. 
Published: May 2009

AbstractMotivation: Liquid chromatography-mass spectrometry (LC/MS) profiling is a promising approach for the quantification of metabolites from complex biological samples. Significant challenges exist in the analysis of LC/MS data, including noise reduction, feature identification/ quantification, feature alignment and computation efficiency.Result: Here we present a set of algorithms for the processing of high-resolution LC/MS data. The major technical improvements include the adaptive tolerance level searching rather than hard cutoff or binning, the use of non-parametric methods to fine-tune intensity grouping, the use of run filter to better preserve weak signals and the model-based estimation of peak intensities for absolute quantification. The algorithms are implemented in an R package apLCMS, which can efficiently process large LC/ MS datasets.Availability: The R package apLCMS is available at www.sph.emory.edu/apLCMS.Contact: tyu8@sph.emory.eduSupplementary information: Supplementary data are available at Bioinformatics online.
PESTAS: a web server for EST analysis and sequence mining
Authors: Nam Seong-Hyeuk , Kim Dae-Won , Jung Tae-Sung , Choi Young-Sang , Kim Dong-Wook , Choi Han-Suk , Choi Sang-Haeng , Park Hong-Seog 
Published: May 2009

Abstract
Summary: We have developed a web server for the high-throughput annotation of expressed sequence tags (ESTs) called pipeline for EST analysis service (PESTAS). PESTAS processes entire datasets with an automated pipeline of 13 analytic services, then deposits the data into the MySQL database and transforms it into three kinds of reports: preprocessing, assembling and annotation. All annotated information is provided to the scientist and can be downloaded through a web browser. To get more relevant functional annotation results, a curation function was introduced with which biologists can easily change the best-hit annotation information. We included a gene chip module that detects gene expression differences between libraries by comparing accession number counts from BLAST search results. PESTAS also provides access to the pathway information of KEGG, which is useful for mapping the relationships among networks of annotated enzymes, and is especially valuable for those researchers interested in biological pathways.
Availability: PESTAS is available at http://pestas.kribb.re.kr/
Supplementary information: Supplementary data are available at http://pestas.kribb.re.kr/pestas.jsp.
Contact: odysseus@kribb.re.kr
Cost‐effectiveness of biological therapy for Crohn’s disease: Markov cohort analyses incorporating United Kingdom patient‐level cost data
Authors: BODGER K. , KIKUCHI T. , HUGHES D. 
Published: May 2009

SummaryBackground  Anti‐TNF‐alpha agents for Crohn's disease (CD) have good clinical efficacy but high acquisition cost compared to rival drugs.Aim  To assess the cost‐effectiveness of infliximab and adalimumab for Crohn’s disease from the perspective of the UK NHS, incorporating recent trial and observational data.Methods  Lifetime Markov analyses constructed to simulate quality‐adjusted life‐years (QALYs) and costs. CD was represented by four health‐states representing: Full response, partial response, nonresponse, surgery and death. The course of CD under standard care was based on the Olmsted county cohort. Systematic review identified ACCENT I (infliximab) and CHARM (adalimumab) as sources for efficacy data. We modelled an intention‐to‐treat strategy for biologics including surgical rates based on observational data, cost estimates from our UK dataset and utilities from an algorithm converting CDAI to EQ‐5D utilities.Results  The incremental cost‐effectiveness ratios (ICERs) compared to standard care for 1‐year of treatment with infliximab or adalimumab were £19 050 and £7190 per QALY gained, respectively. Lifetime therapy was dominated by standard care. Analyses over shorter time horizons, matched to treatment duration, resulted in unfavourable ICERs.Conclusion  The model suggests acceptable ICERs for biological agents when considering a lifetime horizon with periods of up to 4 years continuous therapy. As with all economic evaluations, the results may not be generalizable beyond the perspective of analysis.
Association between entero‐hepatic Helicobacter species and Crohn’s disease: a prospective cross‐sectional study
Authors: LAHARIE D. , ASENCIO C. , ASSELINEAU J. , BULOIS P. , BOURREILLE A. , MOREAU J. , BONJEAN P. , LAMARQUE D. , PARIENTE A. , SOULÉ J.‐C. , CHARACHON A. , COFFIN B. , PEREZ P. , MÉGRAUD F. , ZERBIB F. 
Published: May 2009

SummaryBackground  The pathogenesis of Crohn’s disease (CD) involved microbial factors. Some Helicobacter species, the so‐called entero‐hepatic Helicobacters (EHH), can naturally colonize the intestinal surface and have been detected in humans.Aim  To look for an association between CD and the presence of EHH DNA in intestinal biopsies.Methods  Two groups of patients were included prospectively in a multicentre cross‐sectional study: CD patients with an endoscopic post‐operative recurrence within 2 years following a surgical resection and controls screened for colorectal polyps or cancer. Intestinal biopsies were taken for Helicobacter culture and Helicobacter 16S DNA detection. If positive, the EHH species were identified with specific PCRs, sequencing and denaturing gradient gel electrophoresis.Results  In the 165 included patients (73 CD and 92 controls), Helicobacter cultures were negative. PCR was positive in 44% of CD and 47% of controls. After age‐adjustment, CD was significantly associated with EHH in intestinal biopsies (OR = 2.58; 95%CI: 1.04–6.67). All EHH species detected were identified as Helicobacter pullorum and the closely related species Helicobacter canadensis.Conclusion  Crohn’s disease is associated with the presence of EHH species DNA in intestinal biopsies after adjustment for age. Whether these species play a role in the pathophysiology of CD remains to be determined.
QTL for resistance to Salmonella carrier state confirmed in both experimental and commercial chicken lines
Authors: Calenge F. , Lecerf F. , Demars J. , Feve K. , Vignoles F. , Pitel F. , Vignal A. , Velge P. , Sellier N. , Beaumont C. 
Published: May 2009

SummaryThe ability of chickens to carry Salmonella without displaying disease symptoms is responsible for Salmonella propagation in poultry stocks and for subsequent human contamination through the consumption of contaminated eggs or meat. The selection of animals more resistant to carrier state might be a way to decrease the propagation of Salmonella in poultry stocks and its transmission to humans. Five QTL controlling variation for resistance to carrier state in a chicken F2 progeny derived from the White Leghorn inbred lines N and 61 had been previously identified using a selective genotyping approach. Here, a second analysis on the whole progeny was performed, which led to the confirmation of two QTL on chromosomes 2 and 16. To assess the utility of these genomic regions for selection in commercial lines, we tested them together with other QTL identified in an [N×61] × N backcross progeny and with the candidate genes SLC11A1 and TLR4. We used a commercial line divergently selected for either low or high carrier‐state resistance both in young chicks and in adult hens. In divergent chick lines, one QTL on chromosome 1 and one in the SLC11A1 region were significantly associated with carrier‐state resistance variations; in divergent adult lines, one QTL located in the major histocompatibility complex on chromosome 16 and one in the SLC11A1 region were involved in these variations. Genetic studies conducted on experimental lines can therefore be of potential interest for marker‐assisted selection in commercial lines.
Trajectory analysis of the lower Brent Group (Jurassic), Northern North Sea: contrasting depositional patterns during the advance of a major deltaic system
Authors: Bullimore S. A. , Helland‐Hansen W. 
Published: May 2009

ABSTRACTTrajectory analysis is an alternative approach to systems tract analysis in unravelling the sequence stratigraphic development of sedimentary successions. Whereas the latter anticipates a succession of the depositional history in terms of a given order of systems tracts, trajectory analysis combines trajectory classes in any order, thus providing a more flexible interpretation of the depositional evolution with fewer a priori assumptions about the type or the nature of the mechanisms driving sequence development. The overall regressive part of the Brent Delta (Middle Jurassic, Northern North Sea) has been analysed using this approach. The distribution, thicknesses and stacking patterns of facies associations have been analysed to unravel the trajectorial behaviour of the system. In proximal areas (Oseberg domain), thin shoreface/foreshore packages associated with a prograding strandplain are overlain by upper delta‐plain (floodplain) and distributary channel deposits. Flat or descending regressive trajectories can explain the stratigraphic development in this area. A short distance to the north (Huldra domain), the presence of thicker shoreface/foreshore packages and lower delta‐plain sediments suggests a low‐angle ascending regressive trajectory. In more distal areas (Gullfaks and Visund domains), a higher rate of aggradation leads to the development of even thicker shoreface/foreshore packages and the development of lagoons and bays in the lower delta‐plain realm. Alternating high‐ and low‐angle ascending regressive trajectories can explain the distal development.