bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of Environmental Conditions on Performance of Image Recognition-Based Lane Departure Warning System
Authors: Hadi Mohammed , Sinha Prasoon , Easterling John R.
Published: November 2007

Lane departure warning systems (LDWS) provide an effective counter-measure against road departure crashes. Much commercial development of these systems has concentrated on image processing-based systems. Because these systems depend on the detection and tracking of lane markings, it is logical to hypothesize that the visibility of the markings under different weather and lighting conditions may significantly influence the performance of LDWS. Work was done to determine the effects of environmental conditions such as rain and lighting on LDWS performance with typical lane-marking installations on limited-access facilities. The main performance measure used in this study is the efficacy rate (ER). This is defined as the ratio of the number of instances in which the lane departure warning device is able to provide lane crossing alarms in all instances in which an LDWS-equipped vehicle crosses the lane markings. The results indicate that in most cases the ER of the LDWS under dry and light rain conditions is 100%. However, it was found that performance of LDWS of lane markings was affected significantly by heavy rain conditions at night for typical lane-marking installations. With heavy-rain night conditions, most of the observed ER values were between 0% and 30%. It appears that the ER associated with night rain conditions increases with increased lane-marking retroreflectivity. Dusk conditions were found to drop the ER of LDWS by 15% to 18%. At a few locations that had yellow lane markings near the end of their service lives or had yellow markings on concrete pavements, LDWS had difficulty detecting the markings because of the low level of contrast between the yellow markings and the pavement.
Dependence of Cooperative Vehicle System Performance on Market Penetration
Authors: Shladover Steven E. , Polatkan Gungor , Sengupta Raja , VanderWerf Joel , Ergen Mustafa , Bougler Benedicte
Published: November 2007

Cooperative vehicle systems (CVS) can provide intelligent transportation systems services such as probe vehicle information and hazard warnings by exchanging data among suitably equipped vehicles as they travel. The sensitivity of the performance of CVS to the market penetration of suitably equipped vehicles is explained by using Monte Carlo analyses and simulations of wireless message propagation. The CVS functions are implemented by using wireless vehicle-vehicle data communications, which can be successful only when other equipped vehicles exist within wireless range to receive the messages and relay them to further vehicles. These relays may be accomplished by direct wireless transmission to nearby vehicles, but they may also be facilitated by transport relay, by which vehicles traveling in the opposite direction carry the messages and rebroadcast them to the vehicles that they pass. The effectiveness of both direct and transport relay mechanisms as a function of wireless communication range, market penetration, and traffic density and their influence on the speed of message propagation is shown. The direct relay is most effective with a high density of equipped vehicles, but when the density of equipped vehicles is low, the relays become much more dependent on the slower transport relay. When the market penetration is low early in the development of CVS, the most promising use cases are likely to be those that do not require rapid message propagation.
Characterization of brainstem peptide YY (PYY) neurons
Authors: Glavas Maria M. , Grayson Bernadette E. , Allen Summer E. , Copp Daniel R. , Smith M. Susan , Cowley Michael A. , Grove Kevin L.
Published: November 2007

Peptide YY (PYY), a member of the NPY superfamily of peptides, is predominantly synthesized by the colon and is thought to act on both the gut and brain to modulate energy homeostasis. Although neurons expressing PYY mRNA have also been reported in the brainstem, little is known about their physiological role and study of their projections has been problematic due to crossreactivity of PYY antibodies with NPY. In the present study we examined the localization of central PYY cell bodies in the mouse, rat, and monkey. In addition, efferent projections and afferent inputs of central PYY neurons were examined in rodents. Central PYY projections were examined by immunohistochemistry in the NPY knockout mouse, or with an NPY‐preabsorbed PYY antibody in the rat to avoid any crossreactivity with NPY. In all species investigated PYY‐immunoreactive (ir) cell bodies were localized exclusively to the gigantocellular reticular nucleus (Gi) of the rostral medulla. The highest density of PYY fibers was present within the solitary tract nucleus, specifically within the dorsal and lateral aspects. PYY fibers were also concentrated within the dorsal motor nucleus of the vagus and the hypoglossal nucleus. In addition, both orexin and melanin‐concentrating hormone fibers made numerous close appositions with PYY cell bodies in the Gi. Collectively, the projection pattern and association with orexigenic neuropeptides suggest that brainstem PYY neurons may play a role in energy homeostasis through a coordinated effect on visceral, motor, and sympathetic output targets. J. Comp. Neurol. 506:194–210, 2008. © 2007 Wiley‐Liss, Inc.
Origin of calretinin‐containing, vesicular glutamate transporter 2‐coexpressing fiber terminals in the entorhinal cortex of the rat
Authors: Wouterlood Floris G. , Aliane Verena , Boekel Amber J. , Hur Elizabeth E. , Zaborszky Laszlo , Barroso‐Chinea Pedro , Härtig Wolfgang , Lanciego José L. , Witter Menno P.
Published: November 2007

The entorhinal cortex of the rat (EC) contains a dense fiber plexus that expresses the calcium‐binding protein calretinin (CR). Some CR fibers contain vesicular glutamate transporter 2 (VGluT2, associated with glutamatergic neurotransmission). CR‐VGluT2 coexpressing fibers may have an extrinsic origin, for instance, the midline thalamic nucleus reuniens. Alternatively, they may belong to cortical interneurons. We studied the first possibility with anterograde and retrograde neuroanatomical tracing methods combined with CR and VGluT2 immunofluorescence and confocal laser scanning. The alternative possibility was studied with in situ hybridization fluorescence histochemistry for VGluT2 mRNA combined with CR immunofluorescence. In the anterograde tracing experiments, we observed many labeled reuniens fibers in EC expressing CR. Some of these labeled fibers contained immunoreactivity for VGluT2 and CR. In the complementary retrograde tracing experiments, we found retrogradely labeled cell bodies in nucleus reuniens of the thalamus that coexpressed CR. We also examined the colocalization of VGluT2 and CR in the entorhinal cortex by using in situ hybridization and CR immunofluorescence. In these experiments, we observed CR‐immunopositive cortical neurons that coexpressed VGluT2. For the same sections, with CR as the principal marker and parvalbumin as a control marker, we found that parvalbumin neurons were negative for VGluT2 mRNA. Thus, CR‐VGluT2‐expressing axon terminals in EC belong to two sources: projection fibers from the thalamus and axon collaterals of local interneurons. VGluT2 expression is linked to the synaptic transmission of the excitatory neurotransmitter glutamate, so these thalamic CR‐VGluT2 projection neurons and entorhinal CR‐VGluT2 interneurons should be regarded as excitatory. J. Comp. Neurol. 506:359–370, 2008. © 2007 Wiley‐Liss, Inc.
The relevance of the fetal and neonatal period for the development of novelty preferences, learning, habituation and hemispheric specialization
Authors: Turkewitz Gerald
Published: November 2007

The concept of instinct has been largely based on thinking which relies on an either or approach to determining the genesis of information required for the development of behavior patterns. In part, in response to criticisms of dichotomous views by Schneirla and Lehrman adherents of the view that there exist two distinct sources of information, that is, genetic or environmental (and all of the variants of this nomenclature including its most modern and currently popular form, that is, hard or soft wired) have modified their stance by positing that all characteristics are products of both. They therefore maintain that the task for analysis is parceling out the amount contributed by each source. Gottlieb's approach to an understanding of the development of various characteristics undercut this view by pointing out the inextricable relationship between the various components at all levels of organization. His view gives prenatal and early postnatal events particular relevance for explicating the intertwined nature of developmental processes. In this essay I will present suggestions from a variety of studies which explore and instantiate some of these complex relationships with regard to, novelty preferences, learning, habituation, and cognitive functioning and its' hemispheric specialization. I will also provide examples of how the unique characteristics of early stages of development promote particular types of epigenesis. © 2007 Wiley Periodicals, Inc. Dev Psychobiol 49: 780–787, 2007.
Adults with dyslexia demonstrate attentional orienting deficits
Authors: Buchholz Judy , Aimola Davies Anne
Published: November 2007

Alerting, orienting and executive control of attention are investigated in five adult cases of dyslexia. In comparison with a control group, alerting and executive control were found to be generally intact for each case. Two spatial cueing tasks were employed. For the task requiring target detection, orienting difficulties were evident only in peripheral locations. While orienting attention to parafoveal stimuli was intact for this detection task, it was found to be impaired for the discrimination task. These results are discussed with respect to the methodological differences of the two tasks. It is suggested that the observed orienting deficit may be specific to adjusting the size of attentional focus in individuals with dyslexia, and that this could contribute to the reading difficulties observed. Copyright © 2007 John Wiley & Sons, Ltd.
Gamma knife stereotactic radiosurgery for salivary gland neoplasms with base of skull invasion following neutron radiotherapy
Authors: Douglas James G. , Goodkin Robert , Laramore George E.
Published: November 2007

Background.

Our aim was to examine the outcome of patients treated with a planned gamma knife boost after completion of neutron radiotherapy for salivary gland neoplasms involving the base of skull.

Methods.

Thirty‐four patients with salivary gland neoplasms involving the base of skull were treated from 2001 to 2005 at our institution. These results were compared with a similar historical group treated at our institution from 1984 to 2000. The patients had the following characteristics: median age: 54 years (range, 23–80); median follow‐up period: 20.5 months (range, 4–55); women‐to‐men patient ratio: 1.1:1; histology: 29 adenoid cystic, 3 adenocarcinoma, 1 acinic cell, 1 mucoepidermoid; primary sites of disease: 6 nasopharyngeal, 14 paranasal sinuses, 4 parotid gland, 8 oral cavity, 1 lacrimal gland, and 1 auditory canal. All patients had gross residual disease at the time of treatment. The median neutron dose prescribed to isocenter was 19.2 nGy and the median dose to the effected temporal tip was 11.98 nGy. The median prescribed gamma knife dose was 12 Gy to the 50% isodose line. The median number of isocenters was 17. The median target volume treated was 12.4 cm3 (range, 1.9–28.9) with a median total volume treated of 18.3 cm3 (range, 5.9–53.9).

Results.

The 24‐month and 40‐month Kaplan–Meier estimated local control was 82% versus 81% (24 months) and 82% versus 39% (40 months; p = .04) for the gamma knife treated group versus historical controls (n = 61). Two of the 4 failures in the gamma knife–treated group occurred outside the boosted area. Complications were no greater in the gamma knife–treated group than in those treated with neutron radiotherapy alone.

Conclusions.

Patients with primary salivary gland neoplasms that involve the base of skull and are treated with neutron radiotherapy alone are at high risk of local recurrence. A gamma knife boost improves local control and adds little additional toxicity. These preliminary results suggest that all patients with salivary neoplasms and base of skull invasion should be considered for a gamma knife boost after primary treatment with neutron radiotherapy. © 2007 Wiley Periodicals, Inc. Head Neck, 2008
Human CMV immediate‐early enhancer: a useful tool to enhance cell‐type‐specific expression from lentiviral vectors
Authors: Gruh Ina , Wunderlich Stephanie , Winkler Monica , Schwanke Kristin , Heinke Jennifer , Blömer Ulrike , Ruhparwar Arjang , Rohde Bettina , Li Ren‐Ke , Haverich Axel , Martin Ulrich
Published: November 2007

Background

Lentiviral vectors are attractive delivery tools for gene therapy, especially in terminally differentiated target cells. While restriction of gene expression to specific cell populations is of particular importance, highly efficient cell‐type‐specific gene expression after viral gene transfer so far has been hampered by low levels of transgene expression.

Methods

Addressing this problem, we have integrated the human cytomegalovirus (CMV) immediate‐early enhancer into an ‘advanced’ generation lentiviral vector. Expression cassettes with the reporter gene green fluorescent protein (GFP), combined with the woodchuck hepatitis virus posttranscriptional regulatory element (WPRE) under control of a ubiquitous phosphoglycerate kinase (mouse PGK), cardiomyocyte‐ (human atrial natriuretic factor (ANF), human ventricular myosin light chain (MLC2v)), or type II alveolar epithelial cell (AT‐2)‐specific human surfactant protein C (SP‐C) promoter, were introduced. As insertion of an enhancing element can interfere with the promoter's specificity, expression levels conferred by our enhancer/promoter constructs were evaluated in target and non‐target cells.

Results

Transduction of target cells with human CMV enhancer containing lentiviral vectors resulted in a multiple‐log increase in GFP expression compared to corresponding vectors lacking the human CMV enhancer. In the case of the ANF, the MLC2v, and the SP‐C promoters, tissue‐specific reporter gene expression in cardiomyocytes and in lung AT‐2 cells was maintained, as expression in non‐target cells increased only up to 7‐fold.

Conclusions

The results of this study indicate that lentiviral vectors with the human CMV enhancer conferring efficient cell‐type‐specific gene expression may be useful tools for gene therapy purposes or cell tracing, e.g. to analyze stem cell differentiation in transplantation and co‐culture settings. Copyright © 2007 John Wiley & Sons, Ltd.
An episode of geniospasm in sleep: Toward new insights into pathophysiology?
Authors: Kharraz Bita , Reilich Peter , Noachtar Soheyl , Danek Adrian
Published: November 2007

Polysomnography and needle electromyography were performed on three members of a family with hereditary geniospasm. Electromyography showed simultaneous bilateral discharges exclusively in the mentalis muscle. In one subject we documented a paroxysm of geniospasm during sleep phase 2. This activity ceased with the onset of REM sleep. In view of the mechanism of REM atonia and the bilateral chin EMG discharges, our findings support a supranuclear origin of the peculiar mentalis muscle paroxysms. © 2007 Movement Disorder Society
A compact planar quad‐frequency broad‐band rectangular microstrip patch antenna
Authors: Abdelaziz A. A.
Published: November 2007

A microstrip patch antenna (MPA) with four resonance frequencies is presented. The size of the proposed antenna is reduced using shorting wall and window techniques. The effect of window areas on the shorted antenna parameters has been studied. A planar triple‐frequency developed to quad‐frequency shorted MPA at frequencies 0.9, 1.8, 2.4, and 5.4 GHz has been studied. A bandwidth enhancement is achieved for the 0.9, 2.4, and 5.4 GHz frequencies. Fabrication and measurement of S11 for the proposed antenna has been done. The measured results have been compared with the simulated results using commercial software HFSS version‐8.0. © 2007 Wiley Periodicals, Inc. Microwave Opt Technol Lett 50: 22–24, 2008; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.22974
Two‐dimensional parallel transmission line matrix solver for waveguide analysis
Authors: Altinbasak Caner , Ergene Lale T.
Published: November 2007

Transmission line matrix (TLM) method is a very effective time domain method, which has been used for solving various electromagnetic problems including waveguide structures. In this study, the transient response of a rectangular waveguide is analyzed by using TLM algorithm which is also very suitable for the parallel computing. The problem is extended for parallel environment for the speed up and scalability analysis. Excellent agreement with analytical solution is reported. © 2007 Wiley Periodicals, Inc. Microwave Opt Technol Lett 50: 95–98, 2008; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.22992
Model‐based and model‐free parametric analysis of breast dynamic‐contrast‐enhanced MRI
Authors: Eyal Erez , Degani Hadassa
Published: November 2007

A wide range of dynamic‐contrast‐enhanced (DCE) sequences and protocols, image processing methods, and interpretation criteria have been developed and evaluated over the last 20 years. In particular, attempts have been made to better understand the origin of the contrast observed in breast lesions using physiological models that take into account the vascular and tissue‐specific features that influence tracer perfusion. In addition, model‐free algorithms to decompose enhancement patterns in order to segment and classify different breast tissue types have been developed. This review includes a description of the mechanism of contrast enhancement by gadolinium‐based contrast agents, followed by the current status of the physiological models used to analyze breast DCE‐MRI and related critical issues. We further describe more recent unsupervised and supervised methods that use a range of different common algorithms. The model‐based and model‐free methods strive to achieve scientific accuracy and high clinical performance – both important goals yet to be reached. Copyright © 2008 John Wiley & Sons, Ltd.
Determining protein adducts of fipexide: mass spectrometry based assay for confirming the involvement of its reactive metabolite in covalent binding
Authors: Sleno Lekha , Varesio Emmanuel , Hopfgartner Gérard
Published: November 2007

Fipexide is a nootropic drug, withdrawn from the market due to its idiosyncratic drug reactions causing adverse effects in man. Previous work on its metabolites has identified several potential reactive metabolites which could be implicated in protein binding. Here, we investigated the formation of these metabolites in rat and human hepatocytes. Based on these results, the o‐quinone of fipexide (FIP), formed via the demethylenation reaction through a catechol intermediate, was chosen for further investigation. Studies were then pursued in order to relate this metabolite to protein binding, and thus better understand potential mechanisms for the toxicity of the parent compound. An assay was developed for determining the fipexide catechol‐cysteine adduct in the microsomal protein fractions following in vitro incubations. This method digests the entire protein fraction into amino acids, followed by the detection of the Cys‐metabolite adduct by liquid chromatography/mass spectrometry (LC/MS). We have designed a strategy where drug metabolism taking place in microsomal incubations and involved in protein binding can be assessed after the proteins have been digested, with the detection of the specific amino acid adduct. In this study, the structure of the fipexide adduct was hypothesized using knowledge previously gained in glutathione and N‐acetylcysteine trapping experiments. Acetaminophen was used as a positive control for detecting a drug metabolite‐cysteine adduct by LC/MS. This approach has the potential to be applicable as a protein‐binding assay in early drug discovery without the need for radioactive compounds. Copyright © 2007 John Wiley & Sons, Ltd.
Metacercariae of Galactosomum lacteum (Jägerskiöld, 1896) Looss, 1899 (Heterophyidae) from marine teleosts in the Gulf of Cagliari (southern Sardinia, Italy)
Authors: Culurgioni Jacopo , D'Amico Valeria , Figus Vincenza
Published: November 2007

Galactosomum lacteum (Jägerskiöld, 1896) Looss, 1899 metacercariae, encysted on the optic nerve, on the brain and/or on the muscle and the connective of the pharynx and oesophagus, were found in Spicara maena L., S. flexuosa Rafinesque, 1810, S. smaris L. (Centracanthidae), Gobius cruentatus Gmelin, 1789 (Gobiidae), Symphodus tinca L., S. mediterraneus L. (Labridae), Serranus cabrilla L. (Serranidae), Diplodus sargus L. and D. annularis L. (Sparidae) caught in the Gulf of Cagliari (southern Sardinia, Italy). Excysted specimens were identified by some distinctive morphological features: more or less expanded forebody, depending on whether the specimens were living or fixed; tubular excretory bladder extending to the posterior border of the ovary; two-chambered seminal vesicle; asymmetrical and parenchymatous ventral sucker with lines of spines within its cavity; and unarmed gonotyle. Comparison has been made with the congeneric species metacercaria, G. timondavidi Pearson & Prévot, 1971, also registered in the Mediterranean Sea.
Zur faktoriellen Stabilität der deutschen Version des Questionnaire on the Opinions of the Family (QOF)
Authors: Kallert Thomas W. , Nitsche Ines
Published: November 2007

Zusammenfassung. Die Anzahl von standardisierten Untersuchungsinstrumenten, die Meinungen von Angehörigen zu Ursachen und sozialen Konsequenzen psychischer Störungen erfassen, ist sehr gering. Mit höherem methodischen Aufwand wurde bislang lediglich der in Italien für schizophrene Störungen konzipierte Questionnaire on the Opinions of the Family (QOF) entwickelt. In einem deutschen Forschungsprojekt konnte die Subskalenstruktur des italienischen QOF in einer Gruppe von Angehörigen (N = 161) von Patienten mit rezidivierend depressiven, bipolar affektiven oder schizophrenen Störungen nicht repliziert werden, was die Entwicklung einer ersten deutschen Version dieses Instrumentes (18 Items) veranlasste. Hiermit ließ sich eine 3-Faktoren-Lösung identifizieren, die die Angehörigenmeinungen in die Inhaltsbereiche “soziale Distanz“, “soziale Integration“ und “Orientierung auf Ressourcenoptimierung“ untergliedert. Die faktorielle Stabilität der deutschen QOF-Version wurde in einer weiteren unabhängigen Angehörigenstichprobe (N = 163) sowie an 59 Kontrollpersonen überprüft. Bezogen auf die Faktoren “soziale Distanz“ und “soziale Integration“ erwies sich die faktorielle Stabilität als hoch, wohingegen der dritte Faktor nun um drei Items ergänzt wurde, die soziale Restriktion reflektieren. Resultate aus beiden Teilstudien zum Ausprägungsgrad der Angehörigenmeinungen in den verschiedenen Inhaltsbereichen deuten auf krankheitsspezifische Einstellungsunterschiede hin. Validitätsprüfungen an Angehörigengruppen, deren soziodemographische Charakteristika von den bislang untersuchten Stichproben abweichen, sind notwendig.
Extreme environments in the forests of Ushuaia, Argentina
Authors: D'Antoni Hector , Rothschild Lynn , Schultz Cynthia , Burgess Seth , Skiles J. W.
Published: November 2007

A survey over two mountain slopes (Glaciar Martial and Cerro Guanaco) in the vicinity of Ushuaia (Tierra del Fuego, Argentina) showed normal results for the region in terms of chlorophyll concentration in the leaves of the dominant tree species Nothofagus antarctica, N. pumilio and N. betuloides, and soil variables such as temperature, moisture, pH, and concentration of nitrogen, sodium and potassium. Solar radiation, on the other hand, showed high values of ultraviolet over the 200–400 nm range, suggesting that the environment is extreme in terms of incoming solar radiation. The forest canopy absorbs and/or reflects a significant amount of that radiation. In separate analyses we showed that these tree species contain UV‐absorbing pigments (cyanidin, delphidin, and flavonol glycosides). We submit that the rippled and glossy surface of leaves serves as a reflection/backscattering mechanism that protects their inner structure and function. The presence of krummholz (= twisted, dwarf trees) in the upper end of the forest shows the effects of an extreme environment.
Optical properties of Co silicides: Experiment and density functional theory
Authors: Kudryavtsev Y. V. , Oksenenko V. A. , Lee Y. P. , Rhee J. Y. , Kim Y. D.
Published: November 2007

The dielectric functions of Co2Si, CoSi, and CoSi2 compounds have been measured and compared with the calculated ones. All three compounds have very common features in their density of states, especially near the Fermi level: Co 3d-dominated characteristics with very small amounts of Co and Si sp characteristics. Consequently, the features observed in the optical conductivity (OC) spectra of 0.5–5.0 eV for all the compounds also have very similar characteristics. Since in this energy range both the occupied and empty states involved in the interband-absorption peak formation have a 3d character in an energy range, the major factor contributing to the features observed in the OC spectra is the joint-density-of-states (JDOS) effects, and the optical-transition-matrix elements do not play an important role. Co2Si, whose crystal structure is orthorhombic, has a strong optical anisotropy, as expected. The structural dependence of the electronic band structure for Co silicides has also been evaluated by examining the optical properties of the disordered and the crystalline Co-Si alloy films of the CoSi and CoSi2 stoichiometry. The change in the OC spectra can be explained by “simple” JDOS effects in the DOS curves.
Taking subject knowledge seriously: from professional knowledge recipes to complex conceptualizations of teacher development
Authors: Ellis Viv
Published: November 2007

The specification of various categories of knowledge that teachers should possess has been a historically consistent feature of moves to professionalize school teaching and to argue for individual teachers' professional autonomy. In this article, I suggest that the ways in which subject knowledge has been treated in research‐based recipes for teachers' professional knowledge are often characterized to various degrees by three epistemological problems: the problem of dualism; the problem of objectivism; and the problem of individualism. In place of dualistic, individualistic and objectivist typologies, the article proposes a realistic alternative: a situated view of subject knowledge as emergent within complex and dynamic social systems. A model of this developmental process is offered that represents the development of subject knowledge in practice, that is, teaching a subject in schools. The article concludes with a brief discussion of the practical implications of this view of subject knowledge and teacher development for teacher education programmes.
GlobalANCOVA: exploration and assessment of gene group effects
Authors: Hummel Manuela , Meister Reinhard , Mansmann Ulrich
Published: November 2007

Motivation: Several authors have studied expression in gene sets with specific goals: overrepresentation of interesting genes in functional groups, predictive power for class membership and searches for groups where the constituent genes show coordinated changes in expression under the experimental conditions. The purpose of this article is to follow the third direction. One important aspect is that the gene sets under analysis are known a priori and are not determined from the experimental data at hand. Our goal is to provide a methodology that helps to identify the relevant structural constituents (phenotypical, experimental design, biological component) that determine gene expression in a group.

Results: Gene-wise linear models are used to formalize the structural aspects of a study. The full model is contrasted with a reduced model that lacks the relevant design component. A comparison with respect to goodness of fit is made and quantified. An asymptotic test and a permutation test are derived to test the null hypothesis that the reduced model sufficiently explains the observed expression within the gene group of interest. Graphical tools are available to illustrate and interpret the results of the analysis. Examples demonstrate the wide range of application.

Availability: The R-package GlobalAncova (http://www.bioconductor.org) offers data and functions as well as a vignette to guide the user through specific analysis steps.

Contact:  hummel@ibe.med.uni-muenchen.de
A profile-based deterministic sequential Monte Carlo algorithm for motif discovery
Authors: Liang Kuo-Ching , Wang Xiaodong , Anastassiou Dimitris
Published: November 2007

Motivation: Conserved motifs often represent biological significance, providing insight on biological aspects such as gene transcription regulation, biomolecular secondary structure, presence of non-coding RNAs and evolution history. With the increasing number of sequenced genomic data, faster and more accurate tools are needed to automate the process of motif discovery.

Results: We propose a deterministic sequential Monte Carlo (DSMC) motif discovery technique based on the position weight matrix (PWM) model to locate conserved motifs in a given set of nucleotide sequences, and extend our model to search for instances of the motif with insertions/deletions. We show that the proposed method can be used to align the motif where there are insertions and deletions found in different instances of the motif, which cannot be satisfactorily done using other multiple alignment and motif discovery algorithms.

Availability: MATLAB code is available at http://www.ee.columbia.edu/~kcliang

Contact:  xw2008@columbia.edu
Identification of linked regions using high-density SNP genotype data in linkage analysis
Authors: Lin Guohui , Wang Zhanyong , Wang Lusheng , Lau Yu-Lung , Yang Wanling
Published: November 2007

Motivation: With the knowledge of large number of SNPs in human genome and the fast development in high-throughput genotyping technologies, identification of linked regions in linkage analysis through allele sharing status determination will play an ever important role, while consideration of recombination fractions becomes unnecessary.

Results: In this study, we have developed a rule-based program that identifies linked regions for underlined diseases using allele sharing information among family members. Our program uses high-density SNP genotype data and works in the face of genotyping errors. It works on nuclear family structures with two or more siblings. The program graphically displays allele sharing status for all members in a pedigree and identifies regions that are potentially linked to the underlined diseases according to user-specified inheritance mode and penetrance. Extensive simulations based on the χ2 model for recombination show that our program identifies linked regions with high sensitivity and accuracy. Graphical display of allele sharing status helps to detect misspecification of inheritance mode and penetrance, as well as mislabeling or misdiagnosis. Allele sharing determination may represent the future direction of linkage analysis due to its better adaptation to high-density SNP genotyping data.

Availability:  http://paed.hku.hk/uploadarea/yangwl/html/index.html

Contact:  yangwl@hkucc.hku.hk

Supplementary information: Supplementary data are available at Bioinformatics online.
Evaluation of Applied Plastic Strain Methods for Welding Distortion Prediction
Authors: Zhang L. , Michaleris P. , Marugabandhu P.
Published: November 2007

Large and complex structures such as ship panels generally have various types of welding-induced distortions including angular deformation, longitudinal bending, and buckling. Developing efficient methodologies for modeling welding distortions and residual stresses of large structures plays a critical role in industrial applications. Conventional transient moving source analyses on three-dimensional (3D) finite element models, where millions of degrees of freedom and thousands of time increments are involved, demonstrate the capability to capture all types of welding distortions, but proved to be computational costly. The 2D to 3D applied plastic strain method, where only longitudinal plastic strain resulting from 2D models is mapped to a 3D structural model, successfully predicts buckling and bowing distortions. However, it cannot calculate angular distortion accurately. In this paper, a 3D applied plastic strain method has been developed to predict the welding distortions for structures. In the applied strain method, six components of the plastic strain of each weld are calculated by performing a 3D moving source analysis on a small 3D model with a shorter length, then the plastic strain components of the small models are mapped and superposed to a large 3D structural model to obtain the final distortion results. An interpolation algorithm is developed for mapping between meshes with different densities. The effectiveness of the 3D applied plastic strain method is evaluated by comparing to the distortion results from 3D moving source simulations. The mapping algorithm is verified and the effects of the model size on the distortion results are investigated. The numerical results show that the applied plastic strain method accounts all distortion modes, but is only qualitatively accurate for the prediction of angular distortion.
Perspectives on marine zooplankton lipids
Authors: Kattner G , Hagen W , Lee R F , Campbell R , Deibel D , Falk-Petersen S , Graeve M , Hansen B W , Hirche H J , Jónasdóttir S H , Madsen M L , Mayzaud P , Müller-Navarra D , Nichols P D , Paffenhöfer G -A , Pond D , Saito H , Stübing D , Virtue P
Published: November 2007

We developed new perspectives to identify important questions and to propose approaches for future research on marine food web lipids. They were related to (i) structure and function of lipids, (ii) lipid changes during critical life phases, (iii) trophic marker lipids, and (iv) potential impact of climate change. The first addresses the role of lipids in membranes, storage lipids, and buoyancy with the following key question: How are the properties of membranes and deposits affected by the various types of lipids? The second deals with the importance of various types of lipids during reproduction, development, and resting phases and addresses the role of the different storage lipids during growth and dormancy. The third relates to trophic marker lipids, which are an important tool to follow lipid and energy transfer through the food web. The central question is how can fatty acids be used to identify and quantify food web relationships? With the fourth, hypotheses are presented on effects of global warming, which may result in the reduction or change in abundance of large, lipid-rich copepods in polar oceans, thereby strongly affecting higher trophic levels. The key question is how will lipid dynamics respond to changes in ocean climate at high latitudes?
Effects of stand structure and landscape characteristics on habitat use by birds and small mammals in managed boreal forest of eastern Canada
Authors: St-Laurent Martin-Hugues , Ferron Jean , Hins Caroline , Gagnon Réjean
Published: November 2007

Community structure and relative abundance of 27 species of small mammals and forest birds were compared among three types of residual forest stands and unharvested control forest (CO). Treatments were young and old mosaics (a checkerboard pattern of residual and logged forest units of 85–100 ha each) and megablocks (residual stands of 250–300 ha isolated within a logged area of 2500–3000 ha). Relative abundances were also used to establish habitat use models (HUMs). We found no statistical difference in species relative abundances between treatments and COs, although small sample sizes limited statistical power. HUMs explained a large amount of variation in habitat use for 15 mammal and bird species (mean 57.4 ± 3.5%, ranging between 22.3% and 75.7%). Variance partitioning emphasized the importance of stand structure characteristics as the principal predictors of abundance for censused species. Our results suggested that mosaics and megablocks are both suitable configurations to maintain studied species because no species exhibited lower relative abundances in such residual forest stands than COs. We suggest that residual forest stands planning should shift from a strictly landscape perspective toward a more holistic approach that considers residual forest structure as well as landscape characteristics.
Long-term calcium addition increases growth release, wound closure, and health of sugar maple (Acer saccharum)trees at the Hubbard Brook Experimental Forest
Authors: Huggett Brett A. , Schaberg Paul G. , Hawley Gary J. , Eagar Christopher
Published: November 2007

We surveyed and wounded forest-grown sugar maple ( Acer saccharum Marsh.) trees in a long-term, replicated Ca manipulation study at the Hubbard Brook Experimental Forest in New Hampshire, USA. Plots received applications of Ca (to boost Ca availability above depleted ambient levels) or Al (to compete with Ca uptake and further reduce Ca availability). We found significantly greater total foliar and membrane-associated Ca in foliage of trees in plots fertilized with Ca when compared with trees from Al-addition and control plots (P = 0.005). Coinciding with foliar Ca differences, trees exhibited a significant difference in crown vigor and in percent branch dieback among treatments (P < 0.05), with a trend towards improved canopy health as Ca levels increased. Annual basal area increment growth for the years following treatment initiation (1998–2004) was significantly greater in trees subjected to Ca addition compared with trees in control and Al treatments. Treatment-related improvements in growth were particularly evident after overstory release following a 1998 ice storm. The amount of wound closure was also greatest for trees in Ca-addition plots relative to Al-addition and control plots (P = 0.041). These findings support evidence that ambient Ca depletion is an important limiting factor regarding sugar maple health and highlight the influence of Ca on wound closure and growth following release from competition.
ON THE PROPAGATION OF AN OPTICAL WAVE IN A PHOTOREFRACTIVE MEDIUM
Authors: BIDÉGARAY-FESQUET B. , SAUT J.-C.
Published: November 2007

The aim of this paper is first to review the derivation of a model describing the propagation of an optical wave in a photorefractive medium and to present various mathematical results on this model: Cauchy problem, solitary waves.
Lysophosphatidic Acid Decreases the Nuclear Localization and Cellular Abundance of the p53 Tumor Suppressor in A549 Lung Carcinoma Cells
Authors: Murph Mandi M. , Hurst-Kennedy Jennifer , Newton Victoria , Brindley David N. , Radhakrishna Harish
Published: November 2007

Lysophosphatidic acid (LPA) is a bioactive lipid that promotes cancer cell proliferation and motility through activation of cell surface G protein–coupled receptors. Here, we provide the first evidence that LPA reduces the cellular abundance of the tumor suppressor p53 in A549 lung carcinoma cells, which express endogenous LPA receptors. The LPA effect depends on increased proteasomal degradation of p53 and it results in a corresponding decrease in p53-mediated transcription. Inhibition of phosphatidylinositol 3-kinase protected cells from the LPA-induced reduction of p53, which implicates this signaling pathway in the mechanism of LPA-induced loss of p53. LPA partially protected A549 cells from actinomycin D induction of both apoptosis and increased p53 abundance. Expression of LPA1, LPA2, and LPA3 receptors in HepG2 hepatoma cells, which normally do not respond to LPA, also decreased p53 expression and p53-dependent transcription. In contrast, neither inactive LPA1 (R124A) nor another Gi-coupled receptor, the M2 muscarinic acetylcholine receptor, reduced p53-dependent transcription in HepG2 cells. These results identify p53 as a target of LPA action and provide a new dimension for understanding how LPA stimulates cancer cell division, protects against apoptosis, and thereby promotes tumor progression. (Mol Cancer Res 2007;5(11):1201–11)
The Quantification of Violence Scale: a Simple Method of Recording Significant Violence
Authors: Tyrer Peter , Cooper Sylvia , Herbert Elizabeth , Duggan Conor , Crawford Mike , Joyce Eileen , Rutter Deborah , Seivewright Helen , O'Sullivan Sandra , Rao Bharti , Cicchetti Domenic , Maden Tony
Published: November 2007

Background: Although there are many rating scales recording the incidence and intensity of violence there are none that are specifically concerned with the measurement and assessment of severe violence.

Aims: To develop a scale sensitive to variation centred on severe violence, establish its normative values, test its feasibility, and assess its reliability and validity in different populations.

Method: The Quantification of Violence Scale (QOVS) was developed in two stages. First, a list of 30 commonly eXperienced violent episodes in clinical psychiatric practice were evaluated and tested by weighting each episode by severity. Second, a numerical scale used to record the severity of the episode according to its degree of planning, intent and consequences. Violent episodes in two clinical populations were compared using the Modified Overt Aggression Scale (MOAS) and the preliminary version of the QOVS over periods up to 18 months, following which the numerical scale was developed.

Results: Good (0.60—0.74) to EXcellent (> 0.75) test—retest and inter-rater reliability agreement was obtained with both forms of the scale (intra-class correlations of 0.75 and 0.69 respectively), and similar agreement with MOAS scores was reached (0.67) in clinical populations. The scale was quick and easy to use in practice, and a score defining severe violence (9 on the numerical scale and 16 on the matched scale) was determined.

Conclusions: The QOVS, in its two forms, is a useful measure of recording significant violence in clinical and forensic practice.
The Dialectical Tension Between Individuation and Depersonalization in Cancer Patients' Mediation of Complementary, Alternative and Biomedical Cancer Treatments
Authors: Broom Alex , Tovey Philip
Published: November 2007

Drawing on in-depth interviews with cancer patients, this article examines patients' perspectives on the nature of evidence and the degree to which different understandings of evidence inform decision-making about complementary and alternative medicine (CAM) and biomedical cancer treatments. Results illustrate the ways in which many cancer patients critically engage with questions about the nature of knowledge and the potential pitfalls of science.Their accounts can largely be characterized by a dialectical tension between individuation (espoused by many CAM therapies) and depersonalization (implicit in biomedical care); a tension mediated by individual cancer patient's prognosis and age. On the basis of the results we argue for a re-focusing of social theory to embrace an understanding of grass-roots ontological tensions seen in the experiences of individual cancer patients.The problematic nature of maintaining a narrowly defined `evidence-base' policy on CAM and cancer is also discussed in light of the data.
`Making Up' the Middle-Class Child: Families, Activities and Class Dispositions
Authors: Vincent Carol , Ball Stephen J.
Published: November 2007

In this article we draw on data collected from a recent qualitative project to highlight the enthusiasm of middle-class parents for enrolling their under fives in `enrichment' activities (extra-curricular creative and sporting classes). We seek to identify the part activities play in parental strategies for class reproduction. We first consider the broader issue of children and consumption, drawing out the way in which consumption and leisure activities are highly classed, and focusing on notions of taste and distinction. Then, using examples from the data, we emphasize the sense of urgency and responsibility parents felt concerning their child's development and the classed and gendered involvement of parents. We conclude that enrichment activities are one response to the anxiety and sense of responsibility experienced by middle-class parents as they attempt to `make up' a middle-class child in a social context where reproduction appears uncertain.
Treating the Hotel Like a Home: The Contribution of Studying the Single Location Home/Workplace
Authors: Seymour Julie
Published: November 2007

This article contributes to research on the dynamic of space and social life by examining a comparatively uncommon configuration; that of the single location home/workplace. It draws on an empirical study of family-run hotels, pubs and boarding houses to examine family practices in locations which are both home and business. It considers the ways that the routines of everyday family life are prescribed by the spatial, temporal and legal demands of the business but also how families actively protect against, incorporate and resist such demands. The use of an atypical case will contribute to work on family studies by highlighting the contrasts and similarities with more mainstream settings where the home and paid employment occur in spatially discrete locations. It shows how a family practices perspective can be applicable across theoretical divides and enhance the study of spatiality.
Patterns of adolescent friendships, psychological adjustment and antisocial behavior: The moderating role of family stress and friendship reciprocity
Authors: Ciairano Silvia , Rabaglietti Emanuela , Roggero Antonella , Bonino Silvia , Beyers Wim
Published: November 2007

This study distinguishes different patterns of friendship quality in terms of support from and conflict with friends, and reciprocity. Associations between friendship patterns and adolescents' adjustment (self-perception, expectations for the future, depressive feelings, sense of alienation, lying, disobedience, and aggression) were hypothesized to be moderated by family stress and friendship reciprocity. The sample comprised 622 adolescents of both genders, aged 14 to 20 years. We administered a questionnaire, including the Friendship Quality Scale and a peer nomination, twice at a 6-month interval. We identified two patterns of stable friendships: high (47%) and low (37%) quality. In two other groups, friendship quality changed over time, either from low to high (7%), or from high to low (9%). Of all adolescents, 58% had reciprocal and stable friends and 42% had unilateral friends. Under conditions of high family stress, supportive friendships do not have a positive effect on expectations for success and sense of alienation. Reciprocal friendship promotes higher levels of lying and disobedience but also protects against aggression. Summarizing, the effects of friendship quality can be moderated, either diminishing or exacerbating it, by other context factors.
Moving Management: Theorizing Struggles against the Hegemony of Management
Authors: Spicer André , Böhm Steffen
Published: November 2007

How do groups resist the apparently all-encompassing discourse of management? Rejecting current theories of resistance as `re-appropriation' or `micro-politics', we argue that resistance may be thought of as a hegemonic struggle undertaken by social movements. We identify four major resistance movements that engage with management: unions, organizational misbehaviour, civic movements and civic movement organizations. We argue that these forms of resistance differ in terms of location (civil society or workplace) and strategy (political or infra-political). We chart out the possible interconnections between these different modes of resistance and detail how these interconnections are established. By doing this, the paper provides a framework for understanding the many forms of resistance movements that seek to disrupt the hegemonic discourse of management.