bluuebunny/crossref_metadata_2025 huggingface dataset:
FAST plasma scenarios and equilibrium configurations
Authors: Calabrò G. , Crisanti F. , Ramogida G. , Albanese R. , Cardinali A. , Cucchiaro A. , Granucci G. , Maddaluno G. , Marinucci M. , Nowak S. , Pizzuto A. , Pericoli Ridolfini V. , Pironti A. , Tuccillo A.A. , Zonca F.
Published: April 2009

In this paper we present the fusion advanced studies torus (FAST) plasma scenarios and equilibrium configurations, designed to reproduce the ITER ones (with scaled plasma current) and suitable to fulfil plasma conditions for integrated studies of plasma–wall interaction, burning plasma physics, ITER relevant operation problems and steady state scenarios. The attention is focused on FAST flexibility in terms of both performance and physics that can be investigated: operations are foreseen in a wide range of parameters from high performance H-mode (toroidal field, B
T, up to 8.5 T; plasma current, I
P, up to 8 MA) to advanced tokamak (AT) operation (I
P = 3 MA) as well as full non-inductive current scenario (I
P = 2 MA). The coupled heating power is provided with 30 MW delivered by an ion cyclotron resonance heating system (30–90 MHz), 6 MW by a lower hybrid system (3.7 or 5 GHz) for the long pulse AT scenario, 4 MW by an electron cyclotron resonant heating system (170 GHz − B
T = 6 T) for MHD and localized electron heating control and, eventually, with 10 MW by a negative neutral ion beam (NNBI), which the ports are designed to accommodate. In the reference H-mode scenario FAST preserves (with respect to ITER) fast ion induced as well as turbulence fluctuation spectra, thus addressing the cross-scale couplings issue of micro- to meso-scale physics. The non-inductive scenario at I
P = 2 MA is obtained with 60–70% of bootstrap current and the remaining by LHCD. Predictive simulations of the H-mode scenarios have been performed by means of the JETTO code, using a semi-empirical mixed Bohm/gyro-Bohm transport model. Plasma position and shape control studies are also presented for the reference scenario.
Neoclassical tearing mode control using electron cyclotron current drive and magnetic island evolution in JT-60U
Authors: Isayama A. , Matsunaga G. , Kobayashi T. , Moriyama S. , Oyama N. , Sakamoto Y. , Suzuki T. , Urano H. , Hayashi N. , Kamada Y. , Ozeki T. , Hirano Y. , Urso L. , Zohm H. , Maraschek M. , Hobirk J. , Nagasaki K.
Published: April 2009

The results of stabilizing neoclassical tearing modes (NTMs) with electron cyclotron current drive (ECCD) in JT-60U are described with emphasis on the effectiveness of the stabilization. The range of the minimum EC wave power needed for complete stabilization of an m/n = 2/1 NTM was experimentally identified for two regimes using unmodulated ECCD to clarify the NTM behaviours with different plasma parameters: 0.2 < j
EC/j
BS < 0.4 for W
sat/d
EC ∼ 3 and W
sat/W
marg ∼ 2, and 0.35 < j
EC/j
BS < 0.46 for W
sat/d
EC ∼ 1.5 and W
sat/W
marg ∼ 2. Here, m and n are the poloidal and toroidal mode numbers; j
EC and j
BS the EC-driven current density and bootstrap current density at the mode rational surface; W
sat, W
marg and d
EC the full island width at saturation, marginal island width and full-width at half maximum of the ECCD deposition profile, respectively. Stabilization of a 2/1 NTM using modulated ECCD synchronized with a mode rotation of about 5 kHz was performed, in which it was found that the stabilization effect degrades when the phase of the modulation deviates from that of the ECCD at the island O-point. The decay time of the magnetic perturbation amplitude due to the ECCD increases by 50% with a phase shift of ±50° from the O-point ECCD, thus revealing the importance of the phasing of modulated ECCD. For near X-point ECCD, the NTM amplitude increases, revealing a destabilization effect. It was also found that modulated ECCD at the island O-point has a stronger stabilization effect than unmodulated ECCD by a factor of more than 2.
Diaphragm correction factors for free-air chamber standards for air kerma in x-rays
Authors: Burns D T , Kessler C
Published: April 2009

At present, only a correction factor for photon transmission, k
l, is systematically applied for the entrance diaphragm of free-air chamber standards for air kerma. In the present work, the Monte Carlo code PENELOPE is used to re-evaluate k
l for the BIPM standards and new correction factors are calculated for photon scatter and for fluorescence production in the diaphragm. An additional effect arising from electrons emitted from the diaphragm is shown to be significant at the highest photon energies. The results for the radiation qualities used for international comparisons give a combined diaphragm correction factor k
dia = 0.9980(3) for the BIPM medium-energy standard at 250 kV. This is significantly different from the factor k
l = 0.9996(1) in use at present and it might be concluded that differences are likely to exist for all free-air chamber standards. The effect of using a conical taper at the downstream edge of the diaphragm is shown to be negligible for these radiation qualities.
Shear Stress Induced Reorganization of the Keratin Intermediate Filament Network Requires Phosphorylation by Protein Kinase C ζ
Authors: Sivaramakrishnan Sivaraj , Schneider Jaime L. , Sitikov Albert , Goldman Robert D. , Ridge Karen M.
Published: April 2009

Keratin intermediate filaments (KIFs) form a fibrous polymer network that helps epithelial cells withstand external mechanical forces. Recently, we established a correlation between the structure of the KIF network and its local mechanical properties in alveolar epithelial cells. Shear stress applied across the cell surface resulted in the structural remodeling of KIF and a substantial increase in the elastic modulus of the network. This study examines the mechanosignaling that regulates the structural remodeling of the KIF network. We report that the shear stress–mediated remodeling of the KIF network is facilitated by a twofold increase in the dynamic exchange rate of KIF subunits, which is regulated in a PKC ζ and 14-3-3–dependent manner. PKC ζ phosphorylates K18pSer33, and this is required for the structural reorganization because the KIF network in A549 cells transfected with a dominant negative PKC ζ, or expressing the K18Ser33Ala mutation, is unchanged. Blocking the shear stress–mediated reorganization results in reduced cellular viability and increased apoptotic levels. These data suggest that shear stress mediates the phosphorylation of K18pSer33, which is required for the reorganization of the KIF network, resulting in changes in mechanical properties of the cell that help maintain the integrity of alveolar epithelial cells.
asunderIs a Critical Regulator of Dynein–Dynactin Localization duringDrosophilaSpermatogenesis
Authors: Anderson Michael A. , Jodoin Jeanne N. , Lee Ethan , Hales Karen G. , Hays Thomas S. , Lee Laura A.
Published: April 2009

Spermatogenesis uses mitotic and meiotic cell cycles coordinated with growth and differentiation programs to generate functional sperm. Our analysis of a Drosophila mutant has revealed that asunder (asun), which encodes a conserved protein, is an essential regulator of spermatogenesis. asun spermatocytes arrest during prophase of meiosis I. Strikingly, arrested spermatocytes contain free centrosomes that fail to stably associate with the nucleus. Spermatocytes that overcome arrest exhibit severe defects in meiotic spindle assembly, chromosome segregation, and cytokinesis. Furthermore, the centriole-derived basal body is detached from the nucleus in asun postmeiotic spermatids, resulting in abnormalities later in spermatogenesis. We find that asun spermatocytes and spermatids exhibit drastic reduction of perinuclear dynein–dynactin, a microtubule motor complex. We propose a model in which asun coordinates spermatogenesis by promoting dynein–dynactin recruitment to the nuclear surface, a poorly understood process required for nucleus–centrosome coupling at M phase entry and fidelity of meiotic divisions.
Automatic identification of species-specific repetitive DNA sequences and their utilization for detecting microbial organisms
Authors: Koressaar Triinu , Jõers Kai , Remm Maido
Published: April 2009

Motivation: The concentration of pathogen DNA in biological samples is often very low. Therefore, the sensitivity of diagnostic tests is always a critical factor.

Results: We have developed a novel computational method that identifies species-specific repeats from microbial organisms and automatically designs species-specific PCR primers for these repeats. We tested the methodology on 30 randomly chosen microbial species and we demonstrate that species-specific repeats longer than 300 bp exist in all these genomes. We also used our methodology to design species-specific PCR primers for 86 repeats from five medically relevant microbial species. These PCR primers were tested experimentally. We demonstrate that using species-specific repeats as a PCR template region can increase the sensitivity of PCR in diagnostic tests.

Availability and Implementation: A web version of the method called MultiMPrimer3 was implemented and is freely available at http://bioinfo.ut.ee/multimprimer3/.

Contact:  maido.remm@ut.ee

Supplementary information:  Supplementary data are available at Bioinformatics online.
BIPA: a database for protein–nucleic acid interaction in 3D structures
Authors: Lee Semin , Blundell Tom L
Published: April 2009

Summary:BIPA is a database for protein–nucleic acid interactions in 3D structures. The database provides various physicochemical features of protein–nucleic acid interface such as size, shape, residue propensity, secondary structure composition and intermolecular interactions. The database also contains multiple structural alignments of nucleic acid-binding protein families with annotations of local environments in order to allow definition of features that influence acceptability of mutations at a particular position in a protein family. A web interface has been designed to present the results of these analyses and facilitate navigation of protein–nucleic acid interfaces.

Availability:  http://www-cryst.bioc.cam.ac.uk/bipa

Contact:  semin@cryst.bioc.cam.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Cross species analysis of microarray expression data
Authors: Lu Yong , Huggins Peter , Bar-Joseph Ziv
Published: April 2009

Motivation: Many biological systems operate in a similar manner across a large number of species or conditions. Cross-species analysis of sequence and interaction data is often applied to determine the function of new genes. In contrast to these static measurements, microarrays measure the dynamic, condition-specific response of complex biological systems. The recent exponential growth in microarray expression datasets allows researchers to combine expression experiments from multiple species to identify genes that are not only conserved in sequence but also operated in a similar way in the different species studied.

Results: In this review we discuss the computational and technical challenges associated with these studies, the approaches that have been developed to address these challenges and the advantages of cross-species analysis of microarray data. We show how successful application of these methods lead to insights that cannot be obtained when analyzing data from a single species. We also highlight current open problems and discuss possible ways to address them.

Contact:  zivbj@cs.cmu.edu
MICAlign: a sequence-to-structure alignment tool integrating multiple sources of information in conditional random fields
Authors: Xia Xuefeng , Zhang Song , Su Yu , Sun Zhirong
Published: April 2009

Summary: Sequence-to-structure alignment in template-based protein structure modeling for remote homologs remains a difficult problem even following the correct recognition of folds. Here we present MICAlign, a sequence-to-structure alignment tool that incorporates multiple sources of information from local structural contexts of template, sequence profiles, predicted secondary structures, solvent accessibilities, potential-like terms (including residue–residue contacts and solvent exposures) and pre-aligned structures and sequences. These features, together with a position-specific gap scheme, were integrated into conditional random fields through which the optimal parameters were automatically learned. MICAlign showed improved alignment accuracy over several other state-of-the-art alignment tools based on comparisons by using independent datasets.

Availability: Freely available at http://www.bioinfo.tsinghua.edu.cn/∼xiaxf/micalign for both web server and source code.

Contact:  sunzhr@mail.tsinghua.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
Classification trees for species identification of fish-school echotraces
Authors: Fernandes Paul G.
Published: April 2009

Fernandes, P. G. 2009. Classification trees for species identification of fish-school echotraces. – ICES Journal of Marine Science, 66: 1073–1080. Acoustic surveys provide valuable information on the abundance and distribution of many fish species, but are particularly effective for schooling pelagic fish of commercial importance. However, despite recent advances in multifrequency processing, the technique still requires some subjective judgement when allocating the acoustic data, fish-school echotraces, to particular species—the so-called “scrutiny process”. This is assisted by “ground truth” trawling and operator experience of relating trawl data to echotraces of particular fish schools. In this paper, a method to identify species based on “classification trees” is applied to data from a component of the International North Sea Herring Acoustic Survey. Classification trees may be considered as a variant of decision trees, and have properties that are intuitive to biologists, because they are similar to the keys used for the biological identification of species. The method described here incorporates a multifrequency fish-school filter, image analysis to isolate fish-school echotraces, and finally, a classification-tree system using the multifrequency information from the ground-truthed echotraces that can be translated into a processing tool for objective species allocation. The classification-tree system is compared with the traditional method of expert-based scrutiny. Unlike the latter, however, a measure of uncertainty is attributed to the classification-tree approach and this could be propagated through the acoustic-survey estimation procedure as a component of the total uncertainty in the abundance estimate.
Sound-scattering spectra of steelhead (Oncorhynchus mykiss), coho (O. kisutch), and Chinook (O. tshawytscha) salmonids
Authors: Renfree Josiah S. , Hayes Sean A. , Demer David A.
Published: April 2009

Renfree, J. S., Hayes, S. A., and Demer, D. A. 2009. Sound-scattering spectra of steelhead (Oncorhynchus mykiss), coho (O. kisutch), and Chinook (O. tshawytscha) salmonids. – ICES Journal of Marine Science, 66: 1091–1099. A recently developed method for measuring total target strength (TTS) allows calculation of the absolute scattered energy from fish over a broad-bandwidth signal. This technique uses the ratio of coherent and incoherent sound fields reflected off fish swimming in tanks. In stark contrast to other acoustic methods, this technique works best in reverberant conditions, is self-calibrating, and conveniently provides measurements of sound-scattering spectra for possible target identification. It has been used to successfully characterize the scattering spectra of marine life such as anchovy, sardine, and krill. In this experiment, the broad-bandwidth scattering spectra are characterized for the salmonids steelhead (Oncorhynchus mykiss), coho (Oncorhynchus kisutch), and Chinook (Oncorhynchus tshawytscha). The TTS measurements demonstrate that the scattering spectra for these species are similar, yet discernible. These unique scattering spectra may provide means for acoustically identifying and enumerating such targets in rivers or streams. Having effective acoustic methods for assessing salmon abundance could become a major addition to currently available measurement tools and provide a new, low-impact assessment technique for both commercial and endangered populations.
Using acoustic technology to improve the modelling of the transportation and distribution of juvenile gadoids in the Barents Sea
Authors: Johansen Geir O. , Godø Olav R. , Skogen Morten D. , Torkelsen Terje
Published: April 2009

Johansen, G. O., Godø, O. R., Skogen, M. D., and Torkelsen, T. 2009. Using acoustic technology to improve the modelling of the transportation and distribution of juvenile gadoids in the Barents Sea. – ICES Journal of Marine Science, 66: 1048–1054. Transport of the juvenile stages of gadoids by oceanic currents in the Barents Sea is governed by interactions between the vertical positioning of the fish and the horizontal movement of the water masses. The resulting geographical distribution is important for growth and survival. There is need for observations at proper temporal and spatial scales to improve the representation of vertical distribution in models of the transport process. Stationary acoustic systems are suitable for this purpose. We use such a system to quantify the vertical dynamics of 0-group gadoids with reference to a conceptual model of the temporal variation. The vertical distribution from the conceptual model is applied within a Lagrangian, particle-tracking model. This approach performs better in predicting the geographic distribution of the 0-group during the first 10 months after hatching than a model with random, vertical distribution. The potential of stationary acoustic systems to provide high-quality vertical distributions that improve the predictive power of the transport model is demonstrated. Extensive sampling programmes based on the principles presented here can provide the observations needed to obtain more realistic recruitment–prediction models.
A New Leaf Spot Disease of Calotropis gigantean Caused by Alternaria alternata in Rajasthan, India
Authors: Sain Satish K. , Gour H. N. , Sharma P. , Chowdhry P. N.
Published: April 2009

Madar (Calotropis gigantea) is a medicinally important wild shrub native to India. The seed floss is used for furniture stuffing and the bark for nets and twine. In early 2005, we observed a leaf spot epidemic of madar growing on wasteland sites near the Sikar district of Rajasthan, India. Koch's Postulates were completed. This is the first record of the disease from the Sikar district of the Rajasthan state of India.

Accepted for publication 6 February 2009. Published 31 March 2009.
The Soybean Resistance Gene Rag1 Does Not Protect Against Soybean Cyst and Root-knot Nematodes
Authors: Studham Matthew , MacIntosh Gustavo C. , Avendaño Felicitas , Soh David , Tylka Gregory L.
Published: April 2009

The only well-characterized gene controlling soybean aphid (SBA) resistance is Mi-1.2, a tomato gene that also confers resistance to root-knot nematodes (RKN). Based on similarities between Mi-1.2 and Rag1, which produces a strong antibiosis-type resistance, the authors hypothesized that Rag1 could also provide resistance to nematodes. They evaluated two soybean lines, one carrying the Rag1 gene, and one with no resistance gene, for susceptibility or resistance to soybean cyst nematode (SCN) and RKN.

Accepted for publication 4 March 2009. Published 1 April 2009.
Control of Helicoverpa zea in Tomatoes with Chlorantraniliprole Applied Through Drip Chemigation
Authors: Kuhar Thomas P. , Walgenbach James F. , Doughty Hélène B.
Published: April 2009

Chlorantraniliprole (=Rynaxypyr) is a novel anthranilic diamide insecticide that is of interest to vegetable growers because of its low mammalian toxicity and systemic properties. Field trials were conducted between 2006 and 2008 in North Carolina and Virginia to test the efficacy of chlorantraniliprole as a drip chemigation treatment on tomatoes. Drip chemigation of chlorantraniliprole at various rates and intervals significantly reduced the percentage of tomatoes damaged by tomato fruitworm (Helicoverpa zea) comparable to that typically achieved from multiple foliar applications of insecticides. The best control was achieved with two applications of chlorantraniliprole at 0.074 kg ai/ha, or a single application at 0.099 kg ai/ha. Residual ingestion bioassays showed that chlorantraniliprole was effectively taken up by the roots and was active in leaves up to 66 days after treatment (DAT), active in blossoms up to 22 DAT, but was not active in fruit. Drip chemigation of chlorantraniliprole may offer several advantages over foliar applications, including ease of application, reduced pesticide input into the environment, reduced worker exposure to pesticides, and reduced risk to beneficial arthropods.

Accepted for publication 14 January 2010. Published 7 April 2010.
Effects of food on bacterial community composition associated with the copepod
Acartia tonsa
Dana
Authors: Tang Kam , Dziallas Claudia , Hutalle-Schmelzer Kristine , Grossart Hans-Peter
Published: April 2009

The estuarine copepod
Acartia tonsa
naturally carried diverse strains of bacteria on its body. The bacterial community composition (BCC) remained very conservative even when the copepod was fed different axenic algal species, indicating that the food
per se
did not much affect BCC associated with the copepod. In xenic algal treatments, however, copepod-associated BCC differed with each alga fed, even though the same bacterial source was used to inoculate the algae. In addition, starved copepods taken at the same location but at different times significantly differed in their BCC. Algal species composition and copepod life history therefore serve to regulate BCC associated with copepods, and spatial and temporal variations in algal species composition and copepod origin would alter bacteria–copepod interactions.
Why do species vary in their rate of molecular evolution?
Authors: Bromham Lindell
Published: April 2009

Despite hopes that the processes of molecular evolution would be simple, clock-like and essentially universal, variation in the rate of molecular evolution is manifest at all levels of biological organization. Furthermore, it has become clear that rate variation has a systematic component: rate of molecular evolution can vary consistently with species body size, population dynamics, lifestyle and location. This suggests that the rate of molecular evolution should be considered part of life-history variation between species, which must be taken into account when interpreting DNA sequence differences between lineages. Uncovering the causes and correlates of rate variation may allow the development of new biologically motivated models of molecular evolution that may improve bioinformatic and phylogenetic analyses.
Effective population size and the rate and pattern of nucleotide substitutions
Authors: Woolfit Megan
Published: April 2009

Both the overall rate of nucleotide substitution and the relative proportions of synonymous and non-synonymous substitutions are predicted to vary between species that differ in effective population size (
N
e
). Our understanding of the genetic processes underlying these lineage-specific differences in molecular evolution is still developing. Empirical analyses indicate that variation in substitution rates and patterns caused by differences in
N
e
is often substantial, however, and must be accounted for in analyses of molecular evolution.
Families on the spot: sexual signals influence parent–offspring interactions
Authors: Morales Judith , Alonso-Álvarez Carlos , Pérez Cristóbal , Torres Roxana , Serafino Ester , Velando Alberto
Published: April 2009

In 1950, Tinbergen described the elicitation of offspring begging by the red spot on the bill of parent gulls, and this became a model system for behavioural studies. Current knowledge on colour traits suggests they can act as sexual signals revealing individual quality. However, sexual signals have never been studied simultaneously in relationship to parent–offspring and sexual conflicts. We manipulated the red-spot size in one member of yellow-legged gull pairs and observed their partners' feeding efforts in relationship to offspring begging. In the enlarged-spot group, partners doubled their effort compared with the other groups. Furthermore, in the reduced-spot group, partners provided food in relationship to offspring begging, contrasting with the fixed effort of the partners of enlarged-spot gulls. Manipulated gulls, independently of treatment, provided food in relationship to chicks begging only when the partner's investment was low, and performed a fixed effort when the partner's contribution was high. Results demonstrate that the red spot in yellow-legged gulls functions as a sexual signal and indicate that parental rules are plastic, depending on the information on offer. Previous evidence and this study indicate that this signal is used by all family members to adjust decision rules. The incorporation of sexual signals in parent–offspring interactions can be crucial in understanding intra-familial conflicts.
Fertile organs and
in situ
spores of a new dipteridaceous fern
Hausmannia sinensis
from the Jurassic of northern China
Authors: Wang Yongdong , Zhang Hong
Published: April 2009

As a representative fossil member of the dipteridaceous fern, genus
Hausmannia
was reported worldwide from the Mesozoic strata; however, little is known about the fertile structures, including sporangia and
in situ
spores, of this genus. In this study, a new species
Hausmannia sinensis
was identified from the Middle Jurassic of Nei Mongol (Inner Mongolia), northern China. The specimens are compressions and are well preserved with details of sporangia and
in situ
spores. The leaf laminae are broadly fan-shaped, with an almost entire margin. Primary and lateral veins dichotomously branch to form square or polygonal meshes. Each ultimate mesh bears one to two circular sori of 0.4 mm in diameter. Sori are exindusiate; each sorus contains three to six round to ovoid sporangia. The annulus is developed and oblique, with stomial region present in proximal position. Spores are trilete, circular to oval in shape. Both proximal and distal surfaces are covered with baculate to subverrucate sculptures. Spores range from 20 to 30 μm in diameter (average 28 μm), and are comparable to the dispersed genera
Baculatisporites
Thomas and Pflug and
Apiculatisporis
Potonié and Kremp.
Hausmannia sinensis
represents the first compression species of genus
Hausmannia
form Eurasia, which shows the combination of well-preserved sori, sporangia, annuli and
in situ
spore characters, and is therefore helpful for further understanding the diversity and evolution of the Dipteridaceae fern lineage through time.
Degree dependence in rates of transcription factor evolution explains the unusual structure of transcription networks
Authors: Stewart Alexander J. , Seymour Robert M. , Pomiankowski Andrew
Published: April 2009

Transcription networks have an unusual structure. In both prokaryotes and eukaryotes, the number of target genes regulated by each transcription factor, its
out
-degree, follows a broad tailed distribution. By contrast, the number of transcription factors regulating a target gene, its
in
-degree, follows a much narrower distribution, which has no broad tail. We constructed a model of transcription network evolution through
trans
- and
cis
-mutations, gene duplication and deletion. The effects of these different evolutionary processes on the network structure are enough to produce an asymmetrical
in
- and
out
-degree distribution. However, the parameter values required to replicate known
in
- and
out
-degree distributions are unrealistic. We then considered variation in the rate of evolution of a gene dependent upon its position in the network. When transcription factors with many regulatory interactions are constrained to evolve more slowly than those with few interactions, the details of the
in
- and
out
-degree distributions of transcription networks can be fully reproduced over a range of plausible parameter values. The networks produced by our model depend on the relative rates of the different evolutionary processes. By determining the circumstances under which the networks with the correct degree distributions are produced, we are able to assess the relative importance of the different evolutionary processes in our model during evolution.
Strength determines coalitional strategies in humans
Authors: Benenson Joyce F. , Markovits Henry , Emery Thompson Melissa , Wrangham Richard W.
Published: April 2009

Coalitions enhance survival and reproductive success in many social species, yet they generate contradictory impulses. Whereas a coalition increases the probability of successfully obtaining rewards for its members, it typically requires a division of rewards among members, thereby diminishing individual benefits. Non-human primate data indicate that coalition formation is more likely when an individual's probability of success is low when competing alone. No comparable studies exist for humans. Here we show using a computerized competitive game that humans exhibit a systematic, intuitive strategy for coalition formation based on their own and others' levels of perceived strength, a pattern that resembles coalition formation in chimpanzees,Pan troglodytes. Despite equal expected pay-offs for all strategies, subjects were more likely to form coalitions as their own level of perceived strength waned. Those chosen as coalition partners tended to be stronger individuals or arbitrarily designated ‘friends’. Results suggest a heuristic for human coalitionary decisions that rests on the perception of relative power rather than on the assessment of pay-offs.
The role of natural environments in the evolution of resistance traits in pathogenic bacteria
Authors: Martinez Jose L.
Published: April 2009

Antibiotics are among the most valuable compounds used for fighting human diseases. Unfortunately, pathogenic bacteria have evolved towards resistance. One important and frequently forgotten aspect of antibiotics and their resistance genes is that they evolved in non-clinical (natural) environments before the use of antibiotics by humans. Given that the biosphere is mainly formed by micro-organisms, learning the functional role of antibiotics and their resistance elements in nature has relevant implications both for human health and from an ecological perspective. Recent works have suggested that some antibiotics may serve for signalling purposes at the low concentrations probably found in natural ecosystems, whereas some antibiotic resistance genes were originally selected in their hosts for metabolic purposes or for signal trafficking. However, the high concentrations of antibiotics released in specific habitats (for instance, clinical settings) as a consequence of human activity can shift those functional roles. The pollution of natural ecosystems by antibiotics and resistance genes might have consequences for the evolution of the microbiosphere. Whereas antibiotics produce transient and usually local challenges in microbial communities, antibiotic resistance genes present in gene-transfer units can spread in nature with consequences for human health and the evolution of environmental microbiota that are largely ignored.
Unraveling Transcriptional Control in Arabidopsis Using cis-Regulatory Elements and Coexpression Networks
Authors: Vandepoele Klaas , Quimbaya Mauricio , Casneuf Tine , De Veylder Lieven , Van de Peer Yves
Published: April 2009

Analysis of gene expression data generated by high-throughput microarray transcript profiling experiments has demonstrated that genes with an overall similar expression pattern are often enriched for similar functions. This guilt-by-association principle can be applied to define modular gene programs, identify cis-regulatory elements, or predict gene functions for unknown genes based on their coexpression neighborhood. We evaluated the potential to use Gene Ontology (GO) enrichment of a gene's coexpression neighborhood as a tool to predict its function but found overall low sensitivity scores (13%–34%). This indicates that for many functional categories, coexpression alone performs poorly to infer known biological gene functions. However, integration of cis-regulatory elements shows that 46% of the gene coexpression neighborhoods are enriched for one or more motifs, providing a valuable complementary source to functionally annotate genes. Through the integration of coexpression data, GO annotations, and a set of known cis-regulatory elements combined with a novel set of evolutionarily conserved plant motifs, we could link many genes and motifs to specific biological functions. Application of our coexpression framework extended with cis-regulatory element analysis on transcriptome data from the cell cycle-related transcription factor OBP1 yielded several coexpressed modules associated with specific cis-regulatory elements. Moreover, our analysis strongly suggests a feed-forward regulatory interaction between OBP1 and the E2F pathway. The ATCOECIS resource (http://bioinformatics.psb.ugent.be/ATCOECIS/) makes it possible to query coexpression data and GO and cis-regulatory element annotations and to submit user-defined gene sets for motif analysis, providing an access point to unravel the regulatory code underlying transcriptional control in Arabidopsis (Arabidopsis thaliana).
Ethyl glucuronide in hair. A sensitive and specific marker of chronic heavy drinking
Authors: Morini Luca , Politi Lucia , Polettini Aldo
Published: April 2009

Aims  This study aims to define a cut‐off concentration for ethyl glucuronide in hair to determine if there was a history of heavy drinking.

Settings  Pavia, Italy.

Participants  We analysed hair samples from 98 volunteers among teetotallers, social drinkers and heavy drinkers, whose ethanol daily intake (EDI) was estimated by means of a written questionnaire.

Measurements  Ethyl glucuronide hair concentration (HEtG) was measured by liquid chromatography‐tandem mass spectrometry (lower limit of quantification: 3 pg/mg) using a fully validated method.

Findings  The HEtG level providing the best compromise between sensitivity (0.92) and specificity (0.96) at detecting an EDI of 60 g or higher during the last 3 months was 27 pg/mg. None of the factors examined among those known to affect ethanol metabolism and/or the diagnostic power of other markers of ethanol use or hair analyses, including age, gender, body mass index, tobacco smoke, prevalent beverage, hair colour, cosmetic treatments and hygienic habits was found to influence marker performance significantly. However, the slight differences in HEtG performance observed for some factors (e.g. body mass index, smoke and hair treatments) require further studies on larger groups of individuals in order to assess their influence more precisely.

Conclusions  Our results confirm further that HEtG is a sensitive and specific marker of chronic heavy drinking.
Association of tobacco dependence and quit attempt duration with Rasch‐modeled withdrawal sensitivity using retrospective measures
Authors: Javitz Harold S. , Brigham Janet , Lessov‐Schlaggar Christina N. , Krasnow Ruth E. , Swan Gary E.
Published: April 2009

Aim  To examine whether Rasch modeling would yield a unidimensional withdrawal sensitivity measure correlating with factors associated with successful smoking cessation.

Design  The psychometric Rasch modeling approach was applied to estimate an underlying latent construct (withdrawal sensitivity) in retrospective responses from 1644 smokers who reported quitting for 3 or more months at least once.

Setting  Web‐based, passcode‐controlled self‐administered computerized questionnaire.

Participants  Randomly selected convenience sample of 1644 adult members of an e‐mail invitation‐only web panel drawn from consumer databases.

Measurements  Lifetime Tobacco Use Questionnaire, assessing tobacco use across the life‐span, including demographics and respondent ratings of the severity of withdrawal symptoms experienced in respondents' first and most recent quit attempts lasting 3 or more months.

Findings  Rasch‐modeled withdrawal sensitivity was generally unidimensional and was associated with longer periods of smoking cessation. One latent variable accounted for 74% of the variability in symptom scores. Rasch modeling with a single latent factor fitted withdrawal symptoms well, except for increased appetite, for which the fit was marginal. Demographic variables of education, gender and ethnicity were not related to changes in sensitivity. Correlates of greater withdrawal sensitivity in cessation attempts of at least 3 months included younger age at first quit attempt and indicators of tobacco dependence.

Conclusion  The relationship between tobacco dependence symptoms and Rasch‐model withdrawal sensitivity defines further the relationship between sensitivity and dependence. The findings demonstrate the utility of modeling to create an individual‐specific sensitivity measure as a tool for exploring the relationships among sensitivity, dependence and cessation.
Parents who quit smoking and their adult children's smoking cessation: a 20‐year follow‐up study
Authors: Bricker Jonathan B. , Otten Roy , Liu Jingmin L. , Peterson, Jr Arthur V.
Published: April 2009

Aims  Extending our earlier findings from a longitudinal cohort study, this study examines parents' early and late smoking cessation as predictors of their young adult children's smoking cessation.

Design  Parents' early smoking cessation status was assessed when their children were aged 8 years; parents' late smoking cessation was assessed when their children were aged 17 years. Young adult children's smoking cessation, of at least 6 months duration, was assessed at age 28 years.

Setting  Forty Washington State school districts.

Participants and measurements  Participants were 991 at least weekly smokers at age 17 whose parents were ever regular smokers and who also reported their smoking status at age 28. Questionnaire data were gathered on parents and their children (49% female and 91% Caucasian) in a longitudinal cohort (84% retention).

Findings  Among children who smoked daily at age 17, parents' quitting early (i.e. by the time their children were aged 8) was associated with a 1.7 times higher odds of these children quitting by age 28 compared to those whose parents did not quit [odds ratio (OR) 1.70; 95% confidence interval (CI) 1.23, 2.36]. Results were similar among children who smoked weekly at age 17 (OR 1.91; 95% CI 1.41, 2.58). There was a similar, but non‐significant, pattern of results among those whose parents quit late.

Conclusions  Supporting our earlier findings, results suggest that parents' early smoking cessation has a long‐term influence on their adult children's smoking cessation. Parents who smoke should be encouraged to quit when their children are young.
A radiation hybrid comparative map of ovine chromosome 1 aligned to the virtual sheep genome
Authors: Wu C. H. , Jin W. , Nomura K. , Goldammer T. , Hadfield T. , Dalrymple B. P. , McWilliam S. , Maddox J. F. , Cockett N. E.
Published: April 2009

Ovis aries chromosome one (OAR1) is the largest submetacentric chromosome in the sheep genome and is homologous to regions on human chromosomes 1, 2, 3 and 21. Using the USUoRH5000 ovine whole‐genome radiation hybrid (RH) panel, we have constructed a RH map of OAR1 comprising 102 framework and 75 placed/binned markers across five linkage groups spanning 3759.43 cR5000, with an average marker density of 21.2 cR5000/marker. The alignment of our OAR1 RH map shows good concordance with the recently developed virtual sheep genome, with fewer than 1.86% discrepancies. A comparative map of OAR1 was constructed by examining the location of RH‐mapped orthologues in sheep within the genomes of cow, human, horse and dog. Analysis of the comparative map indicates that conserved syntenies within the five ovine RH linkage groups underwent internal chromosomal rearrangements which, in general, reflect the evolutionary distances between sheep and each of these four species. The ovine RH map presented here integrates all available mapping data and includes new genomic information for ovine chromosome 1.
Genetic diversity of Hungarian indigenous chicken breeds based on microsatellite markers
Authors: Bodzsar N. , Eding H. , Revay T. , Hidas A. , Weigend S.
Published: April 2009

Six local chicken breeds are registered in Hungary and are regarded as Hungarian national treasures: Hungarian White, Yellow and Speckled, and Transylvanian Naked Neck White, Black and Speckled. Three Hungarian academic institutes have maintained these genetic resources for more than 30 years. The Hungarian Yellow, the Hungarian Speckled and the Transylvanian Naked Neck Speckled breeds were kept as duplicates in two separate subpopulations since time of formation of conservation flocks at different institutes. In this study, we investigated genetic diversity of these nine Hungarian chicken populations using 29 microsatellite markers. We assessed degree of polymorphism and relationships within and between Hungarian breeds on the basis of molecular markers, and compared the Hungarian chicken populations with commercial lines and European local breeds. In total, 168 alleles were observed in the nine Hungarian populations. The FST estimate indicated that about 22% of the total variation originated from variation between the Hungarian breeds. Clustering using structure software showed clear separation between the Hungarian populations. The most frequent solutions were found at K = 5 and K = 6, respectively, classifying the Transylvanian Naked Neck breeds as a separate group of populations. To identify genetic resources unique to Hungary, marker estimated kinships were estimated and a safe set analysis was performed. We show that the contribution of all Hungarian breeds together to the total diversity of a given set of populations was lower when added to the commercial lines than when added to the European set of breeds.
Whole genome scan to detect quantitative trait loci for bovine milk protein composition
Authors: Schopen G. C. B. , Koks P. D. , Van Arendonk J. A. M. , Bovenhuis H. , Visker M. H. P. W.
Published: April 2009

The objective of this study was to perform a whole genome scan to detect quantitative trait loci (QTL) for milk protein composition in 849 Holstein–Friesian cows originating from seven sires. One morning milk sample was analysed for the major milk proteins using capillary zone electrophoresis. A genetic map was constructed with 1341 single nucleotide polymorphisms, covering 2829 centimorgans (cM) and 95% of the cattle genome. The chromosomal regions most significantly related to milk protein composition (Pgenome < 0.05) were found on Bos taurus autosomes (BTA) 6, 11 and 14. The QTL on BTA6 was found at about 80 cM, and affected αS1‐casein, αS2‐casein, β‐casein and κ‐casein. The QTL on BTA11 was found at 124 cM, and affected β‐lactoglobulin, and the QTL on BTA14 was found at 0 cM, and affected protein percentage. The proportion of phenotypic variance explained by the QTL was 3.6% for β‐casein and 7.9% for κ‐casein on BTA6, 28.3% for β‐lactoglobulin on BTA11, and 8.6% for protein percentage on BTA14. The QTL affecting αS2‐casein on BTA6 and 17 showed a significant interaction. We investigated the extent to which the detected QTL affecting milk protein composition could be explained by known polymorphisms in β‐casein, κ‐casein, β‐lactoglobulin and DGAT1 genes. Correction for these polymorphisms decreased the proportion of phenotypic variance explained by the QTL previously found on BTA6, 11 and 14. Thus, several significant QTL affecting milk protein composition were found, of which some QTL could partially be explained by polymorphisms in milk protein genes.
Epithelial stem cell‐related alterations in Trichinella spiralis‐infected small intestine
Authors: Walsh R. , Seth R. , Behnke J. , Potten C. S. , Mahida Y. R.
Published: April 2009

Objectives:  Infection of mice with the parasite Trichinella spiralis leads to small intestinal inflammation, characterized by changes in mucosal architecture and subpopulations of epithelial cells. This model has been used to explore changes in the epithelial proliferative cell population and expression of transforming growth factor‐beta (TGF‐β).

Materials and methods:  Histochemical and immunohistochemical studies were undertaken in duodenal samples. Location and number of Ki‐67‐positive cells were assessed using Score and Wincrypts program. Changes in mRNA transcripts were studied by real‐time RT‐PCR.

Results:  T. spiralis infection induced an increase in total number of proliferative (Ki‐67‐positive) cells per half crypt on day 2 post‐infection. Transcription of Math1, a transcription factor required for secretory cell differentiation in the intestine, was up‐regulated on days 6–18 post‐infection. At these time points, numbers of Paneth cells at the crypt base were also increased and the epithelial proliferative zone was shifted up the crypt‐villus axis. Transcription of TGF‐β isoforms within the small intestine was up‐regulated on days 6 and 12 post‐infection, but anti‐TGF‐β antibody treatment had no effect on T. spiralis‐induced changes in mucosal architecture or increase in Paneth/intermediate cells.

Conclusions:  T. spiralis infection promotes an initial increase in small intestinal epithelial proliferation and subsequent cell differentiation along the secretory cell lineage. The resulting increase in numbers of Paneth cells at the crypt base causes the proliferative zone to move up the crypt‐villus axis. Further studies are required to determine the significance of an increase in the expression of TGF‐β transcripts.
Low‐grade inflammation can partly explain the association between the metabolic syndrome and either coronary artery disease or severity of peripheral arterial disease: the CODAM study
Authors: Jacobs M. , Van Greevenbroek M. M. J. , Van Der Kallen C. J. H. , Ferreira I. , Blaak E. E. , Feskens E. J. M. , Jansen E. H. J. M. , Schalkwijk C. G. , Stehouwer C. D. A.
Published: April 2009

Background  Low‐grade inflammation has been hypothesized to underlie the coronary artery disease (CAD) risk associated with the metabolic syndrome, but the evidence is not conclusive. For peripheral arterial disease (PAD; as measured by the ankle‐arm index), this association has not been studied before. The aim was to study whether the association between the metabolic syndrome and CAD or the severity of PAD can be explained by low‐grade inflammation.

Methods  The Cohort study Diabetes and Atherosclerosis Maastricht population includes 574 subjects, with an increased risk of type 2 diabetes, of whom 560 were included in the analyses (343 males; age: 59·5 ± 7·0 years). The inflammation markers that were measured were C‐reactive protein, interleukin 6, soluble vascular cell adhesion molecule‐1, soluble intercellular adhesion molecule‐1 and serum amyloid A. All analyses were adjusted for age, sex and smoking.

Results  Logistic regression showed that the metabolic syndrome was significantly associated with CAD [odds ratio (OR) = 1·86, 95% CI: 1·21; 2·84, P = 0·004]. Further adjustment for inflammatory status, as captured in a combination of the inflammation markers (using an averaged Z‐score), resulted in significant associations of both the metabolic syndrome and inflammatory status with CAD [ORmetabolic syndrome (95% CI) = 1·58 (1·01; 2·46), P = 0·044; ORinflammation (95% CI) = 1·59 (1·14; 2·21), P = 0·007]. Linear regression analysis showed similar results for the ankle‐arm index.

Conclusions  The association between the metabolic syndrome, on the one hand, and prevalence of CAD or the severity of PAD, on the other, can be partly but not completely, 26% and 29% respectively, explained by low‐grade inflammation.