bluuebunny/crossref_metadata_2025 huggingface dataset:
Polymer Holography – New Theory of Image Growth
Authors: Havránek Antonín , Květoň Milan
Published: July 2008

Summary: The image forming process in photopolymer holographic film has been studied thoroughly. Many grow‐curves, i.e. the curves describing the time dependence of the image grow, have been obtained by the special equipment (described in1) under varying conditions. The varying concerns both the changes in film composition and exposition. The S‐type form of the measured grow curves bring out some problem in interpreting them in the framework of the usual diffusion theories of photopolymer image growth. To overcome the problem we add the idea that polymer loses its mobility as it grows to the usual only diffusion theories and put down the more general immobilization‐diffusion theory.2
Synthesis of Polymethacrylates with Carbazole and Benzofuran Pendant Groups for Photovoltaic Applications
Authors: Bogdal Dariusz , Matras Katarzyna , Sanetra Jerzy , Pokladko Monika
Published: July 2008

Summary: The article focuses on the photovoltaic devices made from copolymers of 2‐(carbazol‐9‐yl)ethyl methacrylate (CEM) with benzofuran‐2‐carboxylic acid 2‐(methacryloyloxy)ethyl 6‐(diethylamino)benzo[b]furan‐2‐carboxylate (MB) and poly(3‐decylthiophene) (PDT) or poly(3‐octylthiophene) (P3OT). Photovoltaic cell structure consisted of ITO/active materials/Al. The photophysics of such photoactive devices is based on the photo‐induced charge transfer from donor‐type semiconducting conjugated polymers to the acceptor‐type polymers. The monomer synthesis and polymerization as well as the device fabrication are presented. The copolymers can be spin‐coated from a solution at room temperature without subsequent processing and heat treatment. The photovoltaic properties of the devices are shown.
Light‐Induced Change of Charge Carrier Mobility in Semiconducting Polymers
Authors: Vala Martin , Weiter Martin , Zmeškal Oldřich , Nešpůrek Stanislav , Toman Petr
Published: July 2008

Summary:Light‐driven devices based on reversible change of carrier mobility in semiconducting polymers were investigated. The mobility was altered using a photochromic spiropyran capable of a reversible change of permanent dipole moment and ionization potential. While the latter attribute may result in formation of chemical traps and is more important for matrices with similar ionization potential such as PVK, the former phenomenon results in formation of polar traps and is more pronounced in the case of lower‐band‐gap materials.
A new single‐nucleotide deletion of PMP22 in an HNPP family without recurrent palsies
Authors: Luigetti Marco , Conte Amelia , Madia Francesca , Mereu Maria Lucia , Zollino Marcella , Marangi Giuseppe , Pomponi Maria Grazia , Liberatore Giuseppe , Tonali Pietro Altilio , Sabatelli Mario
Published: July 2008

In this study we describe four patients from the same kindred who were affected by an autosomal‐dominantly inherited peripheral neuropathy. They presented an unusual combination of clinical, electrophysiological, and pathological findings in association with a new mutation of the PMP22 gene. Clinically, three patients had carpal tunnel syndrome symptoms and one patient had late‐onset peroneal atrophy. Motor and sensory nerve conduction velocities were reduced without focal slowing at entrapment sites. Nerve biopsy disclosed diffuse hypomyelination with focal thickening of the myelin sheath in some fibers. Sequence analysis of the PMP22 gene showed a single‐nucleotide deletion (227delG) in the affected patients. This mutation, which has not been reported previously, leads to an open reading frame shift and probably to a truncated and unstable PMP22 protein. We conclude that this novel 227delG mutation of PMP22 gives a mild form of hereditary neuropathy with liability to pressure palsy with atypical clinical and electrophysiological findings. Muscle Nerve, 2008
The influence of substrate peptide length on human β‐tryptase specificity
Authors: Spichalska Bożena , Lesner Adam , Wysocka Magdalena , Śledź Marcin , Łȩgowska Anna , Jaśkiewicz Anna , Miecznikowska Hanna , Rolka Krzysztof
Published: July 2008

Combinatorial chemistry approach was applied to design chromogenic substrates of human β‐tryptase. The most active substrate, Ala‐Ala‐Pro‐Ile‐Arg‐Asn‐Lys‐ANB‐NH2, was selected from among over 9 million heptapeptides. The amide of 5‐amino‐2‐nitrobenzoic acid (ANB‐NH2) attached at the C‐terminus served as a chromophore. In order to determine the optimal length of the tryptase substrate, a series of N‐terminally truncated fragments of this substrate was synthesized. Pro‐Ile‐Arg‐Asn‐Lys‐ANB‐NH2, with the determined value of the specificity constant (kcat/KM) above 9 × 106 M−1 s−1, appeared to be the most specific substrate of tryptase. This substrate was twice as active as the parent heptapeptide substrate. We postulate that the optimal size of the pentapeptide substrate for the interaction with human β‐tryptase is associated with the unique structure of this proteinase, comprising four almost identical monomer subunits arranged in a square flat ring with its substrate pockets faced inside, forming a tetramer with a central pore that can be penetrated by this short peptide. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd.
Augmented Three‐mode MIA‐QSAR Modeling for a Series of Anti‐HIV‐1 Compounds
Authors: Goodarzi Mohammad , Freitas Matheus P.
Published: July 2008

The bioactivities of a series of 2‐amino‐6‐arylsulfonylbenzonitriles and their thio‐ and sulfinyl congeners have been previously modeled by using the MIA‐QSAR approach and the PLS regression method [10]. The present work reports the significant improvement in the prediction ability of the Multivariate Image Analysis applied to Quantitative Structure–Activity Relationship (MIA–QSAR) model by applying Parallel Factor Analysis (PARAFAC) and Artificial Neural Network (ANN) directly to the three‐way array built. This perspective represents an important advance for the accurate prediction of potential drug candidates.
Pathobiology of the human prostate
Authors: Maitland Norman J.
Published: July 2008

Most disorders of the prostate are a result of a loss of essential growth control. The three main pathologies associated with this multifunctional but non‐essential gland – prostatitis, benign prostatic hyperplasia and adenocarcinoma – are thought to originate in the central, transitional and peripheral zones, respectively. Professor Maitland outlines factors that affect the development of prostate cancer and discusses the stem cell hypothesis, which provides explanations for the relative resistance of the tumours to most types of conventional therapy, and for the presence of residual disease after androgen therapy. Copyright © 2008 Wiley Interface Ltd
Cervical schistosomiasis infection in a woman with an abnormal smear
Authors: Okunoye Gbemisola O. , Beattie Gerry J. , AL Nafussi Awatif , Jones Michael
Published: July 2008

The authors present a case history of a Caucasian woman who was found to have cervical schistosomiasis on histology following investigations for an abnormal cervical smear. This case highlights the importance of taking a history of foreign travel, particularly as travel to endemic areas is becoming increasingly common. Copyright © 2008 Wiley Interface Ltd
Age‐ and region‐dependent patterns of Ca2+ accumulations following status epilepticus
Authors: Friedman Linda K. , Saghyan Aleksandr , Peinado Alex , Keesey Robert
Published: July 2008

Elevated Ca2+ concentrations have been implicated in cell death mechanisms following seizures, however, the age and brain region of intracellular Ca2+ accumulations [Ca2+]i, may influence whether or not they are toxic. Therefore, we examined regional accumulations of 45Ca2+ by autoradiography from rats of several developmental stages (P14, P21, P30 and P60) at 5, 14, and 24 h after status epilepticus. To determine whether the uptake was intracellular, Ca2+ was also assessed in hippocampal slices with the dye indicator, Fura 2AM at P14. Control animals accumulated low homogeneous levels of 45Ca2+; however, highly specific and age‐dependent patterns of 45Ca2+ uptake were observed at 5 h. 45Ca2+ accumulations were predominant in dorsal hippocampal regions, CA1/CA2/CA3a, in P14 and P21 rats and in CA3a and CA3c neurons of P30 and P60 rats. Selective midline and amygdala nuclei were marked at P14 but not at P21 and limbic accumulations recurred with maturation that were extensive at P30 and even more so at P60. At 14 h, P14 and P21 rats had no persistent accumulations whereas P30 and P60 rats showed persistent uptake patterns within selective amygdala, thalamic and hypothalamic nuclei, and other limbic cortical regions that continued to differ at these ages. For example, piriform cortex accumulation was highest at P60. Fura 2AM imaging at P14 confirmed that Ca2+ rises were intracellular and occurred in both vulnerable and invulnerable regions of the hippocampus, such as CA2 pyramidal and dentate granule cells. Silver impregnation showed predominant CA1 injury at P20 and P30 but CA3 injury at P60 whereas little or no injury was found in extrahippocampal structures at P14 and P20 but was modest at P30 and maximal at P60. Thus, at young ages there was an apparent dissociation between high 45Ca2+ accumulations and neurotoxicity whereas in adults a closer relationship was observed, particularly in the extrahippocampal structures.
Distribution of local earthquakes in the crust beneath central Lake Baikal
Authors: Suvorov V.D. , Tubanov Ts.A.
Published: July 2008

We have located earthquake hypocenters in the area of central Lake Baikal using the Hypoellipse inversion of direct P traveltimes collected by a local seismological network of seven stations in 2001 through 2005. The location accuracy depends on the agreement between the reference velocity model and the real subsurface. Traveltime residuals have no bearing on the accuracy of depth estimates due to origin time errors.

Hypocenter location with reference to a DSS-derived layered velocity model predicts that the crust is seismogenic between 10 and 22 km. The hypocenters cluster densely in belts trending in NE and SE directions along and across Lake Baikal. Earthquakes become deeper from 10 to 22 km toward the Selenga basin.
Analysis of experimental data on the diffusion coefficients of Fe, Mn, Mg, and Ca in garnets
Authors: Korolyuk V.N. , Lepezin G.G.
Published: July 2008

Experimental data on the diffusion coefficients of Fe, Mn, Mg, and Ca in garnets are generalized. Frequency factors (cm2/s), activation energies (cal/mole), and activation volumes (cm3/mole) are optimized. Based on the compensation law, the dependences of diffusion coefficients on pressure (kbar) and temperature (K) have been derived:
“Area by Area the Machine Unfolds”: The Improvisational Performance Practice of the Art Ensemble of Chicago
Authors: STEINBECK PAUL
Published: July 2008

Since their emergence from the Association for the Advancement of Creative Musicians (AACM) in the 1960s, the members of the Art Ensemble of Chicago have created a distinctive multi-disciplinary performance practice centered on collective improvisation. In this article, I conceptualize Art Ensemble improvisations as networks of group interactions, and I analyze an excerpt from a 1972 Art Ensemble concert recording using a phenomenological perspective informed by my conversations with the group about the performance and by my own experience as an improvised-music practitioner. The analysis focuses on the integration of composed material into the improvisatory process, the functions of stylistic diversity and multi-instrumentalism in Art Ensemble performance practice, and the interactive roles played by Lester Bowie, Roscoe Mitchell, Joseph Jarman, Malachi Favors, and Don Moye.
On nonclassical analytical solutions for advective transport problems
Authors: Selvadurai A. P. S.
Published: July 2008

The paper presents certain nonclassical analytical solutions for describing the one‐dimensional advective transport of a chemical or a contaminant in a fluid‐saturated porous medium. The advective transport is induced by potential flow. The nonclassical nature stems from the influences of time‐dependent boundary concentrations, time‐dependent flow velocities, and the presence of natural attenuation. These analytical results are novel and provide a useful set of solutions for benchmarking computational schemes that have been developed in the literature for solving transport of chemicals and contaminants in fluid‐saturated porous media.
Influence of evaporation and seepage on the convergence of a ventilated cavity
Authors: Gerard Pierre , Charlier Robert , Chambon René , Collin Frédéric
Published: July 2008

In the design of nuclear waste disposals, an important topic concerns the development of an excavated damage zone, where permeability increases. A correct numerical prediction of the coupled processes occurring during excavation is therefore needed. In this paper, a nonclassical hydraulic boundary condition is described. It mixes two modes of water exchanges in partial saturation: seepage and evaporation flows. Seepage flow avoids unphysical water inflow into the rock mass, which might be obtained with usual boundary condition in dilatant geomaterial. Evaporation flows enable the thermodynamical equilibrium between air relative humidity in the cavity and in the rock mass. The numerical modeling of a cavity excavation in dilatant geomaterial is carried out. The results show the influence of the hydraulic boundary condition on the convergence of the cavity. Depending on the value of the transfer coefficient, the proposed numerical model can recover the results obtained with an imposed atmospheric pressure or suction at the cavity wall. The determination of the mass transfer coefficient is thus needed and can be achieved through drying experiments or can be estimated thanks to in situ measurements.
The Rebirth of the Russian Space Program: 50 Years After Sputnik, New Frontiers
Authors: Watkins Nick
Published: July 2008

Every morning, I pass by a large poster in my stairwell of Soviet cosmonaut Yuri Gagarin, who in 1961 became the first person to orbit the Earth. On the poster, which my brother found in Central Asia, Gagarin's helmeted head merges into the curve of the Earth. The poster is a powerful reminder of a time when the Soviet space program was the envy of the world, and when it would have seemed to many people quite likely that by 2008 Soviet cosmonauts would be working on the Moon or be on their way to Mars.
When can we expect extremely high surface temperatures?
Authors: Sterl Andreas , Severijns Camiel , Dijkstra Henk , Hazeleger Wilco , Jan van Oldenborgh Geert , van den Broeke Michiel , Burgers Gerrit , van den Hurk Bart , Jan van Leeuwen Peter , van Velthoven Peter
Published: July 2008

In the Essence project a 17‐member ensemble simulation of climate change in response to the SRES A1b scenario has been carried out using the ECHAM5/MPI‐OM climate model. The relatively large size of the ensemble makes it possible to accurately investigate changes in extreme values of climate variables. Here we focus on the annual‐maximum 2m‐temperature and fit a Generalized Extreme Value (GEV) distribution to the simulated values and investigate the development of the parameters of this distribution. Over most land areas both the location and the scale parameter increase. Consequently the 100‐year return values increase faster than the average temperatures. A comparison of simulated 100‐year return values for the present climate with observations (station data and reanalysis) shows that the ECHAM5/MPI‐OM model, as well as other models, overestimates extreme temperature values. After correcting for this bias, it still shows values in excess of 50°C in Australia, India, the Middle East, North Africa, the Sahel and equatorial and subtropical South America at the end of the century.
Snow anomaly events from historical documents in eastern China during the past two millennia and implication for low‐frequency variability of AO/NAO and PDO
Authors: Chu Guoqiang , Sun Qing , Wang Xiaohua , Sun Junying
Published: July 2008

Models and instrumental data indicate that the spatial and temporal variations of snow cover are significantly related to atmospheric circulation (e.g. the AO/NAO). Here, we present historical snow anomaly events during the past two millennia that provide a unique temporal window to studying long‐term AO/NAO, a prominent phenomenon in wintertime. Direct descriptions such as “no snow during the winter” and “pray God for snow” are interpreted as convincing evidence for snow anomalies. The variations of positive/negative snow abnormal events show clear decadal to century variations during the past two millennia. Based on the previous instrumental research and comparison with other reconstruction data, we suggest the Index of Abnormal Snow (IAS) may be an AO‐like atmospheric variability. The winter during the Medieval Warm Period (MWP) (AD 900–1300) might be strongly influenced by a predominantly positive AO with less snow condition, whereas the Little Ice Age (LIA) (AD 1300–1900) by negative AO concomitant with heavier snowfalls in East Asia. Our data show that a warm climate period (the MWP)/a cold period (the LIA) can be perturbed by a cold spell/a warm spell which are linked with a change in atmospheric circulation. Low‐frequency variability of snow records may be intrinsic to the natural climate system. Although the dynamic mechanisms linking snow anomalies with atmospheric circulation (the AO/NAO, the PDO) is unclear on the decadal to century time scales, Pacific Ocean may play an important role in regulating atmospheric circulations since the IAS is highly correlated with the reconstruction of PDO.
Tyrosine modification enhances metal-ion binding
Authors: Baldwin Graham S. , Bailey Michael F. , Shehan B. Philip , Sims Ioulia , Norton Raymond S.
Published: July 2008

Tyrosine sulfation is a common modification of many proteins, and the ability to phosphorylate tyrosine residues is an intrinsic property of many growth-factor receptors. In the present study, we have utilized the peptide hormone CCK8 (cholecystokinin), which occurs naturally in both sulfated and unsulfated forms, as a model to investigate the effect of tyrosine modification on metal-ion binding. The changes in absorbance and fluorescence emission on Fe3+ binding indicated that tyrosine sulfation or phosphorylation increased the stoichiometry from 1 to 2, without greatly affecting the affinity (0.6–2.8 μM at pH 6.5). Measurement of Ca2+ binding with a Ca2+-selective electrode revealed that phosphorylated CCK8 bound two Ca2+ ions. CCK8 and sulfated CCK8 each bound only one Ca2+ ion with lower affinity. Binding of Ca2+, Zn2+ or Bi3+ to phosphorylated CCK8 did not cause any change in absorbance, but substantially increased the change in absorbance on subsequent addition of Fe3+. The results of the present study demonstrate that tyrosine modification may increase the affinity of metal-ion binding to peptides, and imply that metal ions may directly regulate many signalling pathways.
Application of block diagonal technique to Hamiltonian matrix in performing spin-splitting calculations for GaAs zincblende bulk and quantum wells
Authors: Chen Chun-Nan , Su Wei-Long , Chang Kuo-Ching , Chang Sheng-Hsiung , Chiang Jih-Chen , Lo Ikai , Wang Wan-Tsang , Kao Hsiu-Fen , Lee Meng-En
Published: July 2008

The 2×2 conduction band, 4×4 hole band, and 2×2 spin-orbit split-off band matrices of zincblende semiconductors are obtained by using a block diagonal technique. Importantly, the block diagonal matrices incorporate not only the interband coupling effect but also the bulk inversion asymmetry effect. Analytical expressions for the conduction band spin-splitting energies of GaAs zincblende bulk and quantum wells grown on [001]-, [111]-, and [110]-oriented substrates are formulated by solving the block diagonal matrices. The results show that odd-in-k terms exist in both the bulk and the quantum well expressions due to the bulk inversion asymmetry effect. The presence of these terms is shown to induce the spin-splitting phenomenon.
Experimental evidence and theoretical analysis of photoionized plasma under x-ray radiation produced by an intense laser
Authors: Wang Fei-lu , Fujioka Shinsuke , Nishimura Hiroaki , Kato Daiji , Li Yu-tong , Zhao Gang , Zhang Jie , Takabe Hideaki
Published: July 2008

Photoionized plasma was studied experimentally under laboratory conditions by means of high intensity short pulse lasers. The experiment consists of a gold cavity filled with nitrogen gas. Six laser beams were focused on the inner surface of the gold cavity, thereby generating an almost black-body radiation having temperature of 80eV inside the cavity. This radiation heats the nitrogen gas mainly by means of photoionization. L-shell emissions from N V to N VII have been observed in the wavelength range between 90 and 200Å. A time-dependent Detailed Configuration Accounting computer program has been developed to analyze the experimental spectra. In contrast to standard analysis of astrophysical observations, the evidence for photoionization is inferred from the spectral lines ratios. Comparison between the experimental and simulated line spectra indicates that the radiation heated nitrogen attains temperature of 20–30eV, much lower than the source radiation temperature. Paradoxically, it is also shown that similar line emissions can be reproduced computationally also when the radiation and plasma temperatures both equal approximately 60eV. This misleading result indicates that experimental simulation in laboratory is sometimes necessary to avoid misinterpretation of astrophysical spectra.
Mesoscopic simulation of entanglements using dissipative particle dynamics: Application to polymer brushes
Authors: Goujon Florent , Malfreyt Patrice , Tildesley Dominic J.
Published: July 2008

We use a simple spring-spring repulsion to model entanglements between polymers in dissipative particle dynamics (DPD) simulations. The model is applied to a polymer brushes system to study lubrication. We demonstrate that this method leads to mechanical equilibrium in polymer brushes using the normal DPD time step. The number of bond crossings is calculated to provide a quantitative description of the entanglement. We demonstrate that it is possible to avoid 99% of the bond crossings with the values of spring-spring repulsion that can be used without significantly decreasing the time step. A shear force is applied to the system to study the effect of the decrease in the bond crossings on the structure and rheological properties of the brushes. In particular, we show how the friction coefficient increases with the decrease in the bond crossings of the polymers.
High field electron dynamics in dilute nitride Ga(AsN)
Authors: Spasov S. , Allison G. , Patanè A. , Eaves L. , Tretyakov M. Yu. , Ignatov A. , Hopkinson M. , Hill G.
Published: July 2008

We investigate the high electric field dynamics of conduction electrons in dilute nitride GaAs1−xNx diodes. At low temperature (T<40K), we show that the trapping of hot electrons at localized states leads to low frequency oscillations (<1Hz) of the current at high bias. This slow dynamics is replaced at higher temperatures by a fast response of the current in the subterahertz frequency range, which we relate to the interaction of hot electrons with resonant nitrogen-related states in the conduction band.
A Longitudinal Assessment of an Initial Cohort in a Psychology Learning Community
Authors: Buch Kim , Spaulding Sue
Published: July 2008

Discipline-based learning communities have become a popular strategy for improving student performance and satisfaction. This article describes the goals and features of a university-based, first-year psychology learning community (PLC) implemented in Fall 2003. We also report the results of a longitudinal assessment of the impact of the PLC on student retention and progression, academic performance, cocurricular involvement, and satisfaction with the major. Finally, we discuss the benefits and challenges of implementing a PLC.
“Dealing” with the Central Limit Theorem
Authors: Matz David C. , Hause Emily L.
Published: July 2008

We describe an easy-to-employ, hands-on demonstration using playing cards to illustrate the central limit theorem. This activity allows students to see how a collection of sample means drawn from a nonnormally distributed population will be normally distributed. Students who took part in the demonstration reported it to be helpful in understanding the theorem, enjoyable, and worthwhile. An analysis of open-ended exam questions indicated that students who participated in this demonstration possessed greater understanding of the central limit theorem than those who participated in an alternate demonstration and those who witnessed a standard presentation on the central limit theorem that included no demonstration.
Considering dependence among genes and markers for false discovery control in eQTL mapping
Authors: Chen Liang , Tong Tiejun , Zhao Hongyu
Published: July 2008

Motivation: Multiple comparison adjustment is a significant and challenging statistical issue in large-scale biological studies. In previous studies, dependence among genes is largely ignored. However, such dependence may be strong for some genomic-scale studies such as genetical genomics [also called expression quantitative trait loci (eQTL) mapping] in which thousands of genes are treated as quantitative traits and mapped to different genetical markers. Besides the dependence among markers, the dependence among the expression levels of genes can also have a significant impact on data analysis and interpretation.

Results: In this article, we propose to consider both the mean as well as the variance of false discovery number for multiple comparison adjustment to handle dependence among hypotheses. This is achieved by developing a variance estimator for false discovery number, and using the upper bound of false discovery proportion (uFDP) for false discovery control. More importantly, we introduce a weighted version of uFDP (wuFDP) control to improve the statistical power of eQTL identification. In addition, the wuFDP approach can better control false positives than false discovery rate (FDR) and uFDP approaches when markers are in linkage disequilibrium. The relative performance of uFDP control and wuFDP control is illustrated through simulation studies and real data analysis.

Contacts:  liang.chen@usc.edu; hongyu.zhao@yale.edu

Supplementary information:  Supplementary figures, tables and appendices are available at Bioinformatics online.
A comparative study of survival models for breast cancer prognostication based on microarray data: does a single gene beat them all?
Authors: Haibe-Kains B. , Desmedt C. , Sotiriou C. , Bontempi G.
Published: July 2008

Motivation: Survival prediction of breast cancer (BC) patients independently of treatment, also known as prognostication, is a complex task since clinically similar breast tumors, in addition to be molecularly heterogeneous, may exhibit different clinical outcomes. In recent years, the analysis of gene expression profiles by means of sophisticated data mining tools emerged as a promising technology to bring additional insights into BC biology and to improve the quality of prognostication. The aim of this work is to assess quantitatively the accuracy of prediction obtained with state-of-the-art data analysis techniques for BC microarray data through an independent and thorough framework.

Results: Due to the large number of variables, the reduced amount of samples and the high degree of noise, complex prediction methods are highly exposed to performance degradation despite the use of cross-validation techniques. Our analysis shows that the most complex methods are not significantly better than the simplest one, a univariate model relying on a single proliferation gene. This result suggests that proliferation might be the most relevant biological process for BC prognostication and that the loss of interpretability deriving from the use of overcomplex methods may be not sufficiently counterbalanced by an improvement of the quality of prediction.

Availability: The comparison study is implemented in an R package called survcomp and is available from http://www.ulb.ac.be/di/map/bhaibeka/software/survcomp/.

Contact:  bhaibeka@ulb.ac.be

Supplementary information:  Supplementary data are available at Bioinformatics online.
Transcriptional mechanisms of addiction: role of ΔFosB
Authors: Nestler Eric J
Published: July 2008

Regulation of gene expression is considered a plausible mechanism of drug addiction, given the stability of behavioural abnormalities that define an addicted state. Among many transcription factors known to influence the addiction process, one of the best characterized is ΔFosB, which is induced in the brain's reward regions by chronic exposure to virtually all drugs of abuse and mediates sensitized responses to drug exposure. Since ΔFosB is a highly stable protein, it represents a mechanism by which drugs produce lasting changes in gene expression long after the cessation of drug use. Studies are underway to explore the detailed molecular mechanisms by which ΔFosB regulates target genes and produces its behavioural effects. We are approaching this question using DNA expression arrays coupled with the analysis of chromatin remodelling—changes in the posttranslational modifications of histones at drug-regulated gene promoters—to identify genes that are regulated by drugs of abuse via the induction of ΔFosB and to gain insight into the detailed molecular mechanisms involved. Our findings establish chromatin remodelling as an important regulatory mechanism underlying drug-induced behavioural plasticity, and promise to reveal fundamentally new insight into how ΔFosB contributes to addiction by regulating the expression of specific target genes in brain reward pathways.
Neurogenetic studies of alcohol addiction
Authors: Crabbe John C
Published: July 2008

Neurogenetic studies of alcohol dependence have relied substantially on genetic animal models, particularly rodents. Studies of inbred strains, selectively bred lines and mutants bearing genes whose function has been targeted for over or under expression are reviewed. Studies focused on gene expression changes are the most recent contributors to this literature, and some genetic effects may work through epigenetic mechanisms. In a few instances, interesting parallels have been revealed between genetic risk in humans and studies in non-human animal models. Future approaches are likely to be increasingly complex.
Landscape scale effects of disturbance on riparian vegetation
Authors: RENÖFÄLT BIRGITTA MALM , NILSSON CHRISTER
Published: July 2008

1. Differing responses in riparian species richness and composition to disturbance have been reported as a possible explanation for the differences along and between rivers. This paper explores the role of physical disturbance in shaping landscape‐scale patterns of species distribution in riparian vegetation along a free‐flowing river in northern Sweden.

2. To test whether sensitivity to disturbance varies across large landscapes, we experimentally disturbed riparian vegetation along an entire, free‐flowing river by scouring the soil and the vegetation turf, cutting vegetation, applying waterborne plant litter, and after a period of recovery we measured vegetation responses. The experiment was repeated for two consecutive years.

3. We found no significant effect of disturbance on species composition, but all three forms of disturbance significantly reduced species richness. There was no downstream variation in community responses to disturbance but morphological groups of species responded differently to different kinds of disturbance. Graminoids were most resistant, suppressed only by litter burial. All forms of disturbance except cutting reduced the density of herbaceous species, and species density of trees + shrubs and dwarf shrubs was negatively affected by both scouring and cutting. We also evaluated the effects of disturbance in relation to varying levels of species richness. In nearly all cases, responses were significantly negatively correlated with control plot species richness, and relative responses indicated that species‐rich plots were less resistant to scouring and cutting.

4. Our results suggest that although all disturbance treatments had an effect on species richness, variation in sensitivity to disturbance is not the most important factor shaping landscape‐scale patterns of riparian plant species richness along rivers.
To what extent do microsatellite markers reflect genome‐wide genetic diversity in natural populations?
Authors: VÄLI ÜLO , EINARSSON ANNIKA , WAITS LISETTE , ELLEGREN HANS
Published: July 2008

Microsatellite variability is widely used to infer levels of genetic diversity in natural populations. However, the ascertainment bias caused by typically selecting only the most polymorphic markers in the genome may lead to reduced sensitivity for judging genome‐wide levels of genetic diversity. To test this potential limitation of microsatellite‐based approaches, we assessed the degree of nucleotide diversity in noncoding regions of eight different carnivore populations, including inbred as well as outbred populations, by sequencing 10 introns (5.4–5.7 kb) in 20 individuals of each population (wolves, coyotes, wolverines and lynxes). Estimates of nucleotide diversity varied 30‐fold (7.1 × 10−5 –2.1 × 10−3), with densities of one single nucleotide polymorphism every 112–5446 bp. Microsatellite genotyping (10–27 markers) of the same animals revealed mean multilocus heterozygosities of 0.54–0.78, a 1.4‐fold difference among populations. There was a positive yet not perfect (r2 = 0.70) correlation between microsatellite marker heterozygosity and nucleotide diversity at the population level. For example, point estimates of nucleotide diversity varied in some cases with an order of magnitude despite very similar levels of microsatellite marker heterozygosity. Moreover, at the individual level, no significant correlation was found. Our results imply that variability at microsatellite marker sets typically used in population studies may not accurately reflect the underlying genomic diversity. This suggests that researchers should consider using resequencing‐based approaches for assessing genetic diversity when accurate inference is critical, as in many conservation and management contexts.
Characterization of the porcine Kisspeptins receptor gene and evaluation as candidate for timing of puberty in sows
Authors: Li S. , Ren J. , Yang G. , Guo Y. , Huang L.
Published: July 2008

Kisspeptins receptor (KISS1R), also called GPR54, is a key regulator of puberty in many species. KISS1R and its genetics in pigs remain unexplored. The objective of this study was to characterize the porcine KISS1R gene and evaluate the association of KISS1R mutations with age at puberty in sows. KISS1R was assigned to pig chromosome 2q21‐24 by radiation hybrid mapping. It has a 1438 bp full‐length cDNA and spans 3349 bp genomic sequence consisting of five exons and four introns. Semi‐quantitative RT‐PCR showed that KISS1R transcripts was particularly abundant in the adrenal, prostate, testis, thymus, pituary and hypothalamus. KISS1R mRNA content in the hypothalamus was determined by real‐time quantitative RT‐PCR, and it fluctuated during the oestrous cycle with the highest level in the luteal phase. Anoestrus sows had markedly lower hypothalamic KISS1R mRNA content than cyclic animals. Seven KISS1R SNPs were identified in the founder animals of a White Duroc × Erhualian intercross. One missense mutation (T/C245) showed quite different allele distribution in Chinese and Western breeds. All F0, F1 animals and 367 detailed phenotyped cyclic F2 sows in the White Duroc × Erhualian intercross were genotyped for three KISS1R polymorphisms. No significant association of KISS1R haplotypes and haplotype pairs with age at puberty was observed in the resource population, indicating that mutations in KISS1R are not responsible for divergent age at puberty in White Duroc and Erhualian pigs.
Iron availability affects mcyD expression and microcystin‐LR synthesis in Microcystis aeruginosa PCC7806
Authors: Sevilla Emma , Martin‐Luna Beatriz , Vela Laura , Bes M. Teresa , Fillat Maria F. , Peleato M. Luisa
Published: July 2008

Microcystins are toxins produced by cyanobacteria that entail serious health and environmental problems. They are cyclic heptapeptides synthesized via a mixed polyketide synthase/non‐ribosomal peptide synthetase system called microcystin synthetase. Environmental and nutritional factors that trigger microcystin synthesis are still debated and this work deals with the study of the influence of iron nutritional status on the microcystin synthesis. The results indicate that iron deficiency could be one of the inducing factors of the microcystin synthesis. For the first time, increased transcription of an essential mcy gene and correlative microcystin synthesis has been established. Real‐time PCR analysis of mcyD, and microcystin‐LR synthesis were studied on Microcystis aeruginosa PCC7806 grown in iron‐replete and iron‐deplete media. Iron starvation causes an increase of mcyD transcription, correlative to the increase of microcystin‐LR levels. Four transcription start points were identified for mcyD and two for mcyA, and they are not changed as a consequence of iron deficiency.
Use of guilds for modelling avian responses to vegetation in the Intermountain West (USA)
Authors: Mac Nally Ralph , Fleishman Erica , Thomson James R. , Dobkin David S.
Published: July 2008

Aim Individually focused conservation management of many species is expensive and logistically impractical. Mesofilter conservation methods may facilitate the simultaneous management of multiple species. We used data on distributions of two sets of avian guilds, based on dependence on riparian vegetation and on nest location, to relate occurrence rates to environmental variables. Variables were selected by expert opinion and are likely to be affected by changes in climate and land use.

Location Data were collected from 2001–06 in four adjacent mountain ranges in the central Great Basin (Lander, Nye and Eureka counties, Nevada, USA): the Shoshone Mountains and the Toiyabe, Toquima and Monitor ranges.

Methods Data on occurrence of birds, vegetation composition and vegetation structure were obtained in the field. Geographical coordinates and the normalized difference vegetation index were derived from a digital elevation model and a satellite image. To construct a general model for guilds as a whole, while allowing flexibility for variation in the functional responses of individual species, we applied multivariate adaptive regression splines.

Results The predictive capacity of expert knowledge of relationships between birds and vegetation was inconsistent. Latitude, longitude and elevation may constrain the response of some guilds to changes in vegetation structure and composition. Guild‐based models were useful for modelling species with sparse distributions, which are difficult to model individually. In essence, this method supplements models for the individual species with patterns for the guild to which they belong.

Main conclusions Guilds of birds appeared to have predictable associations with selected attributes of vegetation structure and composition. The criteria by which species are grouped into guilds may affect the success of predictions and management interventions. Our derived models offer the potential to predict effects on the avifauna of management or climate‐driven change in vegetation.
Influence of overweight and obesity on physician costs in adolescents and adults in Ontario, Canada
Authors: Janssen I. , Lam M. , Katzmarzyk P. T.
Published: July 2008

The study purpose was to perform an obesity cost‐of‐illness analysis for individuals living in the province of Ontario, Canada. The participants consisted of a representative sample of 25 038 adults and 2440 adolescents (aged 12–17 years) who participated in the 2000/2001 Canadian Community Health Survey (CCHS). The CCHS data set includes measures of body mass index (BMI) (classified as normal weight, overweight or obese) and relevant covariates (age, income, smoking, alcohol, physical activity). The CCHS data set was linked to the Ontario Health Insurance Plan providers’ database to obtain physician costs for 2002–2003. A two‐part modelling approach was used to calculate and compare the average annual physician cost according to BMI. After adjusting for the covariates, physician costs were not significantly higher in overweight men and women compared with those with a normal weight. Physician costs were 14.7% higher in obese men and 18.2% higher in obese women than in men and women with a normal weight. Average physician costs were comparable in normal‐weight and overweight/obese adolescents ($233 per year in both groups). Because Ontario operates a publicly funded healthcare system, the findings of this study have relevance for other provinces/states and countries that operate similar healthcare systems.
THE POLITICAL TRADE‐OFF BETWEEN ENVIRONMENTAL STRINGENCY AND ECONOMIC DEVELOPMENT IN RURAL AMERICA*
Authors: Lawley Chad , Furtan Hartley
Published: July 2008

ABSTRACT We examine the impact of the political trade‐off between rural economic development and environmental quality on the determination of environmental regulations in the U.S. intensive livestock industry. The political economy model, adapted from Fredriksson (1997), is tested empirically, using state‐level data on environmental regulation of the U.S. livestock sector. We find that state governments respond to greater potential for water pollution with more stringent environmental regulations. Consistent with our political economy model, we also find that states with lower recent growth in per capita income implement less stringent environmental regulations.
A FURTHER EXPLORATION INTO THE ROBUSTNESS OF SPATIAL AUTOCORRELATION SPECIFICATIONS*
Authors: Kato Takafumi
Published: July 2008

ABSTRACT In a recent study, the robustness of linear models with various spatial autocorrelation specifications was assessed through Monte Carlo experiments, and the geostatistical models were concluded to dominate the weight matrix models in the prediction. The present study tests the soundness of this conclusion with a different framework for prediction and presents some experimental results that can call into doubt the dominance of the geostatistical models over the weight matrix models.
The Judicial Transformation of the State: The Case of U.S. Trade Policy, 1974–2004
Authors: CHOREV NITSAN
Published: July 2008

The recent shift in state policies from Keynesianism to neoliberalism was accompanied by a transformation in state structures. The case of trade liberalization in the United States reveals that this structural transformation is of a judicial nature. In 1974, supporters of free trade successfully shifted authority over the management of protectionist claims from Congress to quasi‐judicial bodies in theU.S. executive; in 1994, they successfully strengthened the dispute settlement mechanisms of the World Trade Organization. This judicial transformation indicates a shift from sites where decisions are made by way of political negotiations to sites where judges preside over legal disputes. In the article, I identify the political origins of these judicial transformations and discuss the factors that make judicial sites more favorable to neoliberal policies than political sites.
Harry Potter and the Curse of Headache
Authors: Sheftell Fred , Steiner Timothy J , Thomas Hallie
Published: July 2008

Headache disorders are common in children and adolescents. Even young male Wizards are disabled by them. In this article we review Harry Potter's headaches as described in the biographical series by JK Rowling. Moreover, we attempt to classify them. Regrettably we are not privy to the Wizard system of classifying headache disorders and are therefore limited to the Muggle method, the International Classification of Headache Disorders, 2nd edition (ICHD‐II). Harry's headaches are recurrent. Although conforming to a basic stereotype, and constant in location, throughout the 6 years of his adolescence so far described they have shown a tendency to progression. Later descriptions include a range of accompanying symptoms. Despite some quite unusual features, they meet all but one of the ICHD‐II criteria for migraine, so allowing the diagnosis of 1.6 Probable migraine.
Seizures With Prolonged EEG Abnormalities During an Attack of Migraine Without Aura
Authors: Merlino Giovanni , Valente Mariarosaria , D'Anna Sebastiano , Gigli Gian Luigi
Published: July 2008

The term “migralepsy” indicates a particular condition in which seizures occur during a migraine attack. Several cases of seizures associated with migraine with aura and characterized by transient MRI abnormalities have been published. We report the case of a patient who presented 2 generalized seizures during an attack of migraine without aura and with a transient, diffuse, irregular, high voltage slow activity without clear epileptiform abnormalities in subsequent EEG recordings.
Characterization of the role of a trimeric protein phosphatase complex in recovery from cisplatin‐induced versus noncrosslinking DNA damage
Authors: Vázquez‐Martin Cristina , Rouse John , Cohen Patricia T. W.
Published: July 2008

Cisplatin (cis‐diamminedichloroplatinum) and related chemotherapeutic DNA‐crosslinking agents are widely used to treat human cancers.Saccharomyces cerevisiaewith separate deletions of the genes encoding the trimeric protein serine/threonine phosphatase (Pph)3p–platinum sensitivity (Psy)4p–Psy2p complex, are more sensitive than the isogenic wild‐type (WT) strain to cisplatin. We show here that cisplatin causes an enhanced intra‐S‐phase cell cycle delay in these three deletion mutants. The C‐terminal tail of histone 2AX (H2AX) is hyperphosphorylated in the same mutants, and Pph3p is found to interact with phosphorylated H2AX (γH2AX). After cisplatin treatment is terminated,pph3Δ,psy4Δandpsy2Δmutants are delayed as compared with the WT strain in the dephosphorylation of Rad53p. In contrast, onlypph3Δandpsy2Δcells are more sensitive than WT cells to methylmethanesulfonate, a noncrosslinking DNA‐alkylating agent that is known to cause a Rad53p‐dependent intra‐S‐phase cell cycle delay. Dephosphorylation of Rad53p and the recovery of chromosome replication are delayed in the same mutants, but not inpsy4Δcells. By comparison with their mammalian orthologues, the regulatory subunit Psy4p is likely to inhibit Pph3p catalytic activity. The presence of a weak but active Pph3p–Psy2p complex may allowpsy4Δcells to escape from the Rad53p‐mediated cell cycle arrest. Overall, our data suggest that the trimeric Pph3p–Psy4p–Psy2p complex may dephosphorylate both γH2AX and Rad53p, the differences lying in the more stable interaction of the Pph3 phosphatase with γH2AX as opposed to a transient interaction with Rad53p.