bluuebunny/crossref_metadata_2025 huggingface dataset:
Crystal structures of Lys‐63‐linked tri‐ and di‐ubiquitin reveal a highly extended chain architecture
Authors: Weeks Stephen D. , Grasty Kimberly C. , Hernandez‐Cuebas Lisa , Loll Patrick J.
Published: August 2009

The covalent attachment of different types of poly‐ubiquitin chains signal different outcomes for the proteins so targeted. For example, a protein modified with Lys‐48‐linked poly‐ubiquitin chains is targeted for proteasomal degradation, whereas Lys‐63‐linked chains encode nondegradative signals. The structural features that enable these different types of chains to encode different signals have not yet been fully elucidated. We report here the X‐ray crystal structures of Lys‐63‐linked tri‐ and di‐ubiquitin at resolutions of 2.3 and 1.9 Å, respectively. The tri‐ and di‐ubiquitin species adopt essentially identical structures. In both instances, the ubiquitin chain assumes a highly extended conformation with a left‐handed helical twist; the helical chain contains four ubiquitin monomers per turn and has a repeat length of ∼110 Å. Interestingly, Lys‐48 ubiquitin chains also adopt a left‐handed helical structure with a similar repeat length. However, the Lys‐63 architecture is much more open than that of Lys‐48 chains and exposes much more of the ubiquitin surface for potential recognition events. These new crystal structures are consistent with the results of solution studies of Lys‐63 chain conformation, and reveal the structural basis for differential recognition of Lys‐63 versus Lys‐48 chains. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Improving physical realism, stereochemistry, and side‐chain accuracy in homology modeling: Four approaches that performed well in CASP8
Authors: Krieger Elmar , Joo Keehyoung , Lee Jinwoo , Lee Jooyoung , Raman Srivatsan , Thompson James , Tyka Mike , Baker David , Karplus Kevin
Published: August 2009

A correct alignment is an essential requirement in homology modeling. Yet in order to bridge the structural gap between template and target, which may not only involve loop rearrangements, but also shifts of secondary structure elements and repacking of core residues, high‐resolution refinement methods with full atomic details are needed. Here, we describe four approaches that address this “last mile of the protein folding problem” and have performed well during CASP8, yielding physically realistic models: YASARA, which runs molecular dynamics simulations of models in explicit solvent, using a new partly knowledge‐based all atom force field derived from Amber, whose parameters have been optimized to minimize the damage done to protein crystal structures. The LEE‐SERVER, which makes extensive use of conformational space annealing to create alignments, to help Modeller build physically realistic models while satisfying input restraints from templates and CHARMM stereochemistry, and to remodel the side‐chains. ROSETTA, whose high resolution refinement protocol combines a physically realistic all atom force field with Monte Carlo minimization to allow the large conformational space to be sampled quickly. And finally UNDERTAKER, which creates a pool of candidate models from various templates and then optimizes them with an adaptive genetic algorithm, using a primarily empirical cost function that does not include bond angle, bond length, or other physics‐like terms. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Modeling G protein‐coupled receptors for structure‐based drug discovery using low‐frequency normal modes for refinement of homology models: Application to H3 antagonists
Authors: Rai Brajesh K. , Tawa Gregory J. , Katz Alan H. , Humblet Christine
Published: August 2009

G Protein‐Coupled Receptors (GPCRs) are integral membrane proteins that play important role in regulating key physiological functions, and are targets of about 50% of all recently launched drugs. High‐resolution experimental structures are available only for very few GPCRs. As a result, structure‐based drug design efforts for GPCRs continue to rely on in silico modeling, which is considered to be an extremely difficult task especially for these receptors. Here, we describe Gmodel, a novel approach for building 3D atomic models of GPCRs using a normal mode‐based refinement of homology models. Gmodel uses a small set of relevant low‐frequency vibrational modes derived from Random Elastic Network model to efficiently sample the large‐scale receptor conformation changes and generate an ensemble of alternative models. These are used to assemble receptor–ligand complexes by docking a known active into each of the alternative models. Each of these is next filtered using restraints derived from known mutation and binding affinity data and is refined in the presence of the active ligand. In this study, Gmodel was applied to generate models of the antagonist form of histamine 3 (H3) receptor. The validity of this novel modeling approach is demonstrated by performing virtual screening (using the refined models) that consistently produces highly enriched hit lists. The models are further validated by analyzing the available SAR related to classical H3 antagonists, and are found to be in good agreement with the available experimental data, thus providing novel insights into the receptor–ligand interactions. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Allostery and conformational free energy changes in human tryptophanyl‐tRNA synthetase from essential dynamics and structure networks
Authors: Bhattacharyya Moitrayee , Ghosh Amit , Hansia Priti , Vishveshwara Saraswathi
Published: August 2009

The interdependence of the concept of allostery and enzymatic catalysis, and they being guided by conformational mobility is gaining increased prominence. However, to gain a molecular level understanding of allostery and hence of enzymatic catalysis, it is of utter importance that the networks of amino acids participating in allostery be deciphered. Our lab has been exploring the methods of network analysis combined with molecular dynamics simulations to understand allostery at molecular level. Earlier we had outlined methods to obtain communication paths and then to map the rigid/flexible regions of proteins through network parameters like the shortest correlated paths, cliques, and communities. In this article, we advance the methodology to estimate the conformational populations in terms of cliques/communities formed by interactions including the side‐chains and then to compute the ligand‐induced population shift. Finally, we obtain the free‐energy landscape of the protein in equilibrium, characterizing the free‐energy minima accessed by the protein complexes. We have chosen human tryptophanyl‐tRNA synthetase (hTrpRS), a protein responsible for charging tryptophan to its cognate tRNA during protein biosynthesis for this investigation. This is a multidomain protein exhibiting excellent allosteric communication. Our approach has provided valuable structural as well as functional insights into the protein. The methodology adopted here is highly generalized to illuminate the linkage between protein structure networks and conformational mobility involved in the allosteric mechanism in any protein with known structure. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Design of multispecific protein sequences using probabilistic graphical modeling
Authors: Fromer Menachem , Yanover Chen , Linial Michal
Published: August 2009

In nature, proteins partake in numerous protein– protein interactions that mediate their functions. Moreover, proteins have been shown to be physically stable in multiple structures, induced by cellular conditions, small ligands, or covalent modifications. Understanding how protein sequences achieve this structural promiscuity at the atomic level is a fundamental step in the drug design pipeline and a critical question in protein physics. One way to investigate this subject is to computationally predict protein sequences that are compatible with multiple states, i.e., multiple target structures or binding to distinct partners. The goal of engineering such proteins has been termed multispecific protein design. We develop a novel computational framework to efficiently and accurately perform multispecific protein design. This framework utilizes recent advances in probabilistic graphical modeling to predict sequences with low energies in multiple target states. Furthermore, it is also geared to specifically yield positional amino acid probability profiles compatible with these target states. Such profiles can be used as input to randomly bias high‐throughput experimental sequence screening techniques, such as phage display, thus providing an alternative avenue for elucidating the multispecificity of natural proteins and the synthesis of novel proteins with specific functionalities. We prove the utility of such multispecific design techniques in better recovering amino acid sequence diversities similar to those resulting from millions of years of evolution. We then compare the approaches of prediction of low energy ensembles and of amino acid profiles and demonstrate their complementarity in providing more robust predictions for protein design. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Regional covariation and its application for predicting protein contact patches
Authors: Xu YongBai , Tillier Elisabeth R. M.
Published: August 2009

Correlated mutation analysis (CMA) is an effective approach for predicting functional and structural residue interactions from multiple sequence alignments (MSAs) of proteins. As nearby residues may also play a role in a given functional interaction, we were interested in seeing whether covarying sites were clustered, and whether this could be used to enhance the predictive power of CMA. A large‐scale search for coevolving regions within protein domains revealed that if two sites in a MSA covary, then neighboring sites in the alignment also typically covary, resulting in clusters of covarying residues. The program PatchD(http://www.uhnres.utoronto.ca/labs/tillier/) was developed to measure the covariation between disconnected sequence clusters to reveal patch covariation. Patches that exhibit strong covariation identify multiple residues that are generally nearby in the protein structure, suggesting that the detection of covarying patches can be used in conjunction with traditional CMA approaches to reveal functional interaction partners. Proteins 2010. © 2009 Wiley‐Liss, Inc.
An oven explosion: Lessons learned on PSM applications
Authors: Cazabon Michael D. , Erickson Kirby
Published: August 2009

An explosion occurred at one of our customer's locations in late 1998 involving unburned and partially burned natural gas while the unit was in high fire mode. Investigation of the incident led to many contributing causes, most of which can be categorized broadly as lack of process safety information, failure of a fuel combustion control system, contractor control and lack of management of change.

Combustion systems are found throughout all industries and homes. Code‐based safeguards are thoroughly and adequately described in NFPA. But is the spirit and intent of the code always applied and interpreted safely? Instrumentation application and installation are similarly well described in manufacturer's literature and the ISA standards. But are these systems installed and arranged properly? Is it important to manage change in something as mundane as fuel fired equipment? Is explosion venting on industrial ovens a sound way to limit damage? Is it even possible in all instances? Are there alternatives?

This article highlights the investigation activities, answers these questions, presents conclusions and suggests remedies while showing the applicability of PSM concepts to industries other than the CPI.

This article will describe, in general terms: the process, critical changes in design, key components involved, applicable codes, discoveries during the investigation and solutions deployed during the rebuild to address these issues. © 2009 American Institute of Chemical Engineers Process Saf Prog 2010
Variations in fish assemblages in a tributary of the upper Paraná River, Brazil: A comparison between pre and post‐closure phases of dams
Authors: Gubiani Éder André , Gomes Luiz Carlos , Agostinho Angelo Antonio , Baumgartner Gilmar
Published: August 2009

This paper purposed to evaluate alterations in fish assemblage (structure and species richness) and variations in the abundance of the most abundant species captured in the Piquiri River, due to the closure of Porto Primavera (in 1998; located upstream the Piquiri River mouth) and the Itaipu (in 1982; located downstream) dams in the upper Paraná River. The effects of selected environmental variables were also determined. Fishes were sampled during four distinct periods. Six samplings were conducted in each period, at two different sites (Campina and Apertado). For sampling, gill and trammel nets were used. Species abundances were indexed by catch per unit of effort. Spatial and temporal changes in environmental variables were summarized by a principal components analysis (PCA). To summarize structure of the assemblage, a nonmetric multidimensional scaling (NMS) was used. To test the significance of between‐group differences at each periods and sites we used a multiresponse permutation procedure (MRPP). To test the association between fish assemblage and the environmental variables matrices, we used procrustean superimposition approach. A total of 2693 individuals were caught, belonging to 69 species, 4 orders and 19 families. Species richness differed spatially; the Campina site had greater mean richness (13) per sampling than the Apertado site (10). The structure of the fish assemblages showed significant temporal and spatial variations, which were more evident in the last period at the Apertado site (after the closure of Porto Primavera Dam). Spatial and temporal changes in structure of fish assemblages were not associated to environmental variables. Temporal changes in abundance, both in number and in weight, of the most abundant species were verified in both sites. The lack of migratory species was highlighted, which sharply decreased in the last studied period, when they were replaced by sedentary species. These findings appear to be related to regional factors, such as the decrease of floods registered in the upper Paraná basin, exacerbated by the control prompted by dams. Copyright © 2009 John Wiley & Sons, Ltd.
Estimating spawning habitat availability in flooded areas of the river Waal, the Netherlands
Authors: van de Wolfshaar K. E. , Ruizeveld de Winter A. C. , Straatsma M. W. , van den Brink N. G. M. , de Leeuw J. J.
Published: August 2009

Fish spawning habitat availability in the river Waal is significantly influenced by seasonal and annual variations in discharge. In this paper we develop habitat suitability models, based on a literature survey of spawning preferences of the commonly occurring species roach (Rutilus rutilus), bream (Abramis brama), pikeperch (Sander lucioperca) and bleak (Alburnus alburnus). Within the resulting models water depth, flow velocity, water temperature and vegetation type were the most significant environmental parameters. Spatial data for the parameters were derived from a 2‐D hydrodynamic model and detailed monitoring database. The area of suitable habitat available for spawning was calculated using the HABITAT software, based on species‐specific suitability models and the environmental characteristics of two study sites on the river Waal over a 3 year period (1997–1999). The predicted available spawning area was compared with field data on the recruitment of young fish of each species for the same years and locations. There was a positive relationship between predicted available habitat and observed young of the year (YOY) densities for bream, roach and pikeperch. A negative relationship was recorded between predicted available area and observed YOY densities for bleak. The results indicate that optimal hydrological and hydraulic conditions differ even for species that are widely considered eurytopic. Moreover, annual differences in habitat availability indicate a strong influence of hydrological variability on population dynamics. Copyright © 2009 John Wiley & Sons, Ltd.
Endometrial blood flow is impaired in women with polycystic ovarian syndrome who are clinically hyperandrogenic
Authors: Lam P. , Johnson I. , Raine‐Fenning N.
Published: August 2009

Objectives

To quantify endometrial and subendometrial blood flow in Caucasian women with polycystic ovarian syndrome (PCOS) and to determine whether these values differ according to the phenotypic expression of PCOS.

Methods

Transvaginal pelvic ultrasound was performed on the 3rd–5th day of the menstrual cycle in 36 women with PCOS and 36 controls to examine the endometrial and subendometrial vascularity. The subendometrial and endometrial blood flow indices (vascularizaton index (VI), flow index (FI) and vascularization flow index (VFI)) were measured using three‐dimensional power Doppler angiography. Uterine artery blood flow was assessed through analysis of two‐dimensional (2D) pulsed‐wave Doppler waveforms. Analysis was performed to compare PCOS with non‐PCOS women, and subgroup analysis was performed of the PCOS women categorized according to their phenotypic manifestation.

Results

There were no significant differences in endometrial volume, subendometrial vascularity and uterine artery blood flow between women with PCOS and controls after controlling for body mass index (BMI). On subgroup analysis, compared with anovulatory but clinically normoandrogenic women with polycystic ovaries (PCO) and with controls, women with PCO who were both clinically hyperandrogenic and anovulatory had significantly lower endometrial (VI: 0.57% vs. 1.11% and 0.86%, respectively, both P = 0.01; VFI: 0.14 vs. 0.42 and 0.28, respectively, both P = 0.02) and subendometrial (VI: 1.59% vs. 3.17% and 2.47%, P = 0.01 and 0.02, respectively; VFI: 0.50 vs. 1.67 and 0.96, P = 0.01 and 0.02, respectively) blood flow. Moreover, clinically hyperandrogenic but ovulatory women with PCO also had significantly lower endometrial blood flow (VI: 0.52% vs. 1.11%, P = 0.04) than did anovulatory but clinically normoandrogenic women with PCO. There were no differences in any of the 2D pulsed‐wave Doppler measures of blood flow between the subgroups.

Conclusions

Subendometrial and endometrial blood flow is significantly impaired in women with PCOS who have clinical signs of hyperandrogenism. Copyright © 2009 ISUOG. Published by John Wiley & Sons, Ltd.
Fabrication of Carbon Nanotube/SiO2and Carbon Nanotube/SiO2/Ag Nanoparticles Hybrids by Using Plasma Treatment
Authors: Li Haiqing , Ha Chang-Sik , Kim Il
Published: August 2009

Based on plasma-treated single wall carbon nanotubes (SWCNTs), SWCNT/SiO2and thiol groups-functionalized SWCNT/SiO2hybrids have been fabricated through a sol–gel process. By means of thiol groups, Ag nanoparticles have been in situ synthesized and bonded onto the SiO2shell of SWCNT/SiO2in the absence of external reducing agent, resulting in the stable carbon nanotube/SiO2/Ag nanoparticles hybrids. This strategy provides a facile, low–cost, and green methodology for the creation of carbon nanotube/inorganic oxides-metal nanoparticles hybrids.
Physical and psychosocial functioning following motor vehicle trauma: Relationships with chronic pain, posttraumatic stress, and medication use
Authors: Clapp Joshua D. , Masci Jarod , Bennett Shira A. , Beck J. Gayle
Published: August 2009

Chronic pain and PTSD are known to hold substantial comorbidity following traumatic injury. Although pharmacological agents have been examined in the treatment of pain and PTSD individually, little is known regarding the relationship of medication use with functioning in patients with comorbid conditions. This research examined the relationships of pain, PTSD, and medication use across physical and psychosocial functioning in patients with chronic pain following motor vehicle injury (N=234). Separate analyses were conducted for opioids, SSRIs, and sedative/anxiolytics, respectively. Several relevant effects were noted: (1) Pain evidenced strong associations with reduced functioning across both physical and psychosocial domains, (2) Opioid use held interactive relationships with PTSD across both functioning domains. Specifically, opioids were associated with greater physical impairment in patients without comorbid PTSD. Opioids also were related to greater psychosocial impairment in patients without PTSD while PTSD was associated with greater impairment in patients not using opioids, (3) Opioid use evidenced a marginal interaction with pain on psychosocial functioning. Opioids were associated with greater psychosocial impairment among patients with high‐pain, and high‐pain was associated with greater impairment among opioid users, (4) SSRIs held a marginal interaction with PTSD such that PTSD was related to poorer psychosocial functioning only among individuals not using an SSRI, and (5) Anxiolytic use evidenced a marginal interaction with PTSD on physical functioning although no between‐group differences were noted. These data suggest that PTSD symptomology may be an important consideration in determining treatment modality for patients experiencing pain subsequent to traumatic injury.
Similar distribution of simple sequence repeats in diverse completedHuman Immunodeficiency Virus Type 1genomes
Authors: Chen Ming , Tan Zhongyang , Jiang Jianhui , Li Mingfu , Chen Hongjun , Shen Guoli , Yu Ruqin
Published: August 2009

The survey of simple sequence repeats (SSRs) has been extensively made in eukaryotes and prokaryotes. However, its still rare in viruses. Thus, we undertook a survey of SSRs inHuman Immunodeficiency Virus Type 1(HIV‐1) which is an excellent system to study evolution and roles of SSRs in viruses. Distribution of SSRs was examined in 81 completed HIV‐1 genome sequences which come from 34 different countries or districts over 6 continents. In these surveyed sequences, although relative abundance and relative density exhibit very high similarity, some of these sequences show different preference for most common SSRs and longest SSRs. Our results suggest proportion of various repeat types might be related to genome stability.
Campaign Communications in U.S. Congressional Elections
Authors: DRUCKMAN JAMES N. , KIFER MARTIN J. , PARKIN MICHAEL
Published: August 2009

Electoral campaigns are the foundation of democratic governance; yet scholarship on the content of campaign communications remains underdeveloped. In this paper, we advance research on U.S. congressional campaigns by integrating and extending extant theories of campaign communication. We test the resulting predictions with a novel dataset based on candidate Web sites over three election cycles. Unlike television advertisements or newspaper coverage, Web sites provide an unmediated, holistic, and representative portrait of campaigns. We find that incumbents and challengers differ across a broad range of behavior that reflects varying attitudes toward risk, that incumbents’ strategies depend on the competitiveness of the race, and that candidates link negative campaigning to other aspects of their rhetorical strategies. Our efforts provide researchers with a basis for moving toward a more complete understanding of congressional campaigns.
Effect of capsinoids on energy metabolism in human subjects
Authors: Galgani Jose E. , Ryan Donna H. , Ravussin Eric
Published: August 2009

Capsinoids are non-pungent compounds with molecular structures similar to capsaicin, which has accepted thermogenic properties. To assess the acute effect of a plant-derived preparation of capsinoids on energy metabolism, we determined RMR and non-protein respiratory quotient (NPRQ) after ingestion of different doses of the capsinoids. Thirteen healthy subjects received four doses of the capsinoids (1, 3, 6 and 12 mg) and placebo using a crossover, randomised, double-blind trial. After a 10 h overnight fast as inpatients, RMR was measured by indirect calorimetry for 45 min before and 120 min after ingesting capsinoids or placebo. Blood pressure and axillary temperature were measured before ( − 55 and − 5 min) and after (60 and 120 min) dosing. Before dosing, mean RMR was 6247 (se92) kJ/d and NPRQ was 0·86 (se0·01). At 120 min after dosing, metabolic rate and NPRQ remained similar across the four capsinoids and placebo doses. Capsinoids also had no influence on blood pressure or axillary temperature. Capsinoids provided in four doses did not affect metabolic rate and fuel partitioning in human subjects when measured 2 h after exposure. Longer exposure and higher capsinoids doses may be required to cause meaningful acute effects on energy metabolism.
Prevalence and risk factors for obesity in Balearic Islands adolescents
Authors: Bibiloni Maria del Mar , Martinez Elisa , Llull Rosa , Juarez Maria Daniela , Pons Antoni , Tur Josep A.
Published: August 2009

The aim of this work was to assess the prevalence and risk factors of obesity in the Balearic Islands' adolescents. A cross-sectional nutritional survey was carried out in the Balearic Islands (2007–2008). A random sample (n1231) of the adolescent population (12–17 year old) was interviewed. Anthropometric measurements, two non-consecutive 24 h recalls and a general questionnaire incorporating questions related to sociodemographic and lifestyle variables including the physical activity questionnaire were used. The prevalence of overweight was 19·9 % (boys) and 15·5 % (girls), and obesity 12·7 % (boys) and 8·5 % (girls). The main risk factors associated with a higher prevalence of obesity were low parental education level (boys OR: 3·47; 95 % CI: 1·58, 7·62; girls OR: 3·29; 95 % CI: 1·38, 7·89), to skip meals (boys OR: 4·99; 95 % CI: 2·1, 11·54; girls OR: 2·20; 95 % CI: 0·99, 4·89), age (12–13-year-old boys; OR: 2·75; 95 % CI: 1·14, 6·64), attention to mass media (television (TV)+radio; boys OR: 1·50; 95 % CI: 0·81, 2·84; girls OR: 2·06; 95 % CI: 0·91, 4·68), short sleep (boys OR: 3·42; 95 % CI: 0·88, 13·26), low parental socioeconomic status (girls OR: 3·24, 95% CI: 1·04, 10·05 ) and smoking (girls OR: 2·51; 95 % CI: 0·88, 7·13). A programme of action including school healthy education and promotion programmes targeted at parents and adolescents are needed. These programmes may be mainly focused to increase educational level, to make the adolescents to be aware of to skip meals and to smoke are not appropriate methods to reduce the risk of obesity, but the usefulness is to do not eat while watching TV, to sleep 8–10 h/d and to be physically active.
Chinese tea consumption is associated with longer telomere length in elderly Chinese men
Authors: Chan Ruth , Woo Jean , Suen Eddie , Leung Jason , Tang Nelson
Published: August 2009

Environmental and lifestyle factors that affect oxidative stress and inflammation may influence telomere length (TL). There are limited data to relate the effect of dietary components on TL. The present study examined the association between food groups and TL in a sample of elderly Chinese. In a sample of 2006 Chinese (976 men and 1030 women) aged 65 years and over, TL was measured by quantitative real-time PCR and daily intake of food groups was assessed by a validated FFQ. Linear regression and analysis of covariance were used to examine the association between food group intake and TL, with adjustment for demographic and lifestyle factors. In men, only Chinese tea consumption was significantly associated with TL after adjustment for demographics and lifestyle factors (P = 0·002). Mean difference in TL for those in the highest quartile of Chinese tea consumption (>3 cups/d or >750 ml/d) as compared with those in the lowest quartile of Chinese tea consumption ( ≤ 0·28 cups/d or ≤ 70 ml/d) was 0·46 kb, corresponding to approximately a difference of 5 years of life. In women, intake of fats and oils was borderline and negatively associated with TL after adjustment for demographic and lifestyle factors (P = 0·037). In conclusion, Chinese tea consumption was positively associated with TL in elderly Chinese men.
The cereal rust miteAbacarus hystrix(Acari: Eriophyoidea) is a complex of species: evidence from mitochondrial and nuclear DNA sequences
Authors: Skoracka A. , Dabert M.
Published: August 2009

The cereal rust miteAbacarus hystrix(Nalepa), a significant pest of grasses, has been regarded as one of a few exceptions among eriophyoid mites with reference to the pattern of host plant utilization. At least 60 grass species have been recorded as its hosts. Thus, the mite has long been considered as a host generalist in which host specialization would not be likely to evolve. However, recent studies have revealed that host-associated specialization is possible inA. hystrix. Here, we aimed to discriminate between the three populations ofA. hystrixassociated with the different hosts (namely quackgrass, ryegrass and smooth brome) on the basis of mitochondrial (COI) and nuclear (D2 region of 28S rDNA) DNA sequences. The phylogenetic trees obtained with the maximum likelihood analysis of both COI and D2 region data sets showed that host-adapted strains ofA. hystrixform distinct clades. Furthermore, on the COI nucleotide tree, the quackgrass- and brome-associated strains were internally divided each into two well-supported monophyletic clusters. The nucleotide D2 region data set tree showed that brome-associated strain is polyphyletic in origin. There is clear co-variation of DNA results with earlier morphological and ecological traits, as well as the results of crossing experiments. We showed that reproductively incompatible strains ofA. hystrixexhibit more than 20% sequence divergence in the COI gene and 0.2% sequence divergence in the D2 28S rDNA. Our results did not confirm the placement of three host-associated strains ofA. hystrixwithin one, ostensibly generalist, species.
Quantitative variation and biosynthesis of hindgut volatiles associated with the red turpentine beetle, Dendroctonus valens LeConte, at different attack phases
Authors: Shi Z.-H. , Sun J.-H.
Published: August 2009

The red turpentine beetle (RTB), Dendroctonus valens LeConte, is a destructive invasive forest pest in China. For such tree-killing species, how to initiate a volatile-mediated mass attack is of great importance during the course of establishment. To understand the hindgut volatile production mechanism underlying mass attack initiated by RTB, coupled gas chromatography-mass spectrometry and 13C-labelled precursors were applied to explore the quantitative variation and biosynthesis of volatiles associated with RTB at different attack phases. Five previously described volatiles, trans-verbenol, myrtenol, cis-verbenol, myrtenal and verbenone, were identified and quantified from extracts of female and male hindguts, with the first two compounds as the major components and the latter three as minor constituents. In newly emerged females and males, only minute amounts of these compounds were detected. The quantity of volatiles from female adults significantly increased after they fed on bolts. Male adults also yielded larger quantities of volatiles after they joined females in galleries, which suggested that RTB males could accelerate the mass colonization on host trees. We also confirmed that RTB produced the five volatiles through oxidizing the major host monoterpene, α-pinene, but not synthesized de novo since products were labeled without 13C. The implication of this study in understanding the successful invasion of RTB is discussed.
Stock Market Mispricing: Money Illusion or Resale Option?
Authors: Chen Carl R. , Lung Peter P. , Wang F. Albert
Published: August 2009

We examine two hypotheses to explain stock mispricing: i) the money illusion hypothesis (Modigliani and Cohn (1979)) and ii) the resale option hypothesis (Scheinkman and Xiong (2003)). We find that the money illusion hypothesis may explain the level, but not the volatility, of mispricing in the U.S. market. In contrast, the stock resale option hypothesis, which stems from heterogeneous beliefs about future dividend growth rates and short-sale constraints, can explain both the level and the volatility of mispricing. The evidence suggests that while the two hypotheses complement each other in explaining the level of mispricing, the resale option hypothesis provides a more coherent explanation for asset price bubbles, in which extraordinarily high price levels are often accompanied by excessive volatility and frenzied trading.
Evidence for structural abnormalities of the human habenular complex in affective disorders but not in schizophrenia
Authors: Ranft K. , Dobrowolny H. , Krell D. , Bielau H. , Bogerts B. , Bernstein H.-G.
Published: August 2009

Background

The habenular complex is composed of important relay nuclei linking the limbic forebrain to the midbrain and brain stem nuclei. Based on clinical observations, experiments with animals and theoretical considerations, it has been speculated that this brain area might be involved in psychiatric diseases (i.e. schizophrenia and depression). However, evidence in favour of this hypothesis is still lacking because the human habenular complex has rarely been studied with regard to mental illness.

Method

We examined habenular volumes in post-mortem brains of 17 schizophrenia patients, 14 patients with depression (six patients with major depression and eight patients with bipolar depression) and 13 matched controls. We further determined the neuronal density, cell number and cell area of the medial habenular nuclei of the same cohorts using a counting box and a computer-assisted instrument.

Results

Significantly reduced habenular volumes of the medial and lateral habenula were estimated in depressive patients in comparison to normal controls and schizophrenia patients. We also found a reduction in neuronal cell number and cell area in depressive patients for the right side compared to controls and schizophrenia patients. No such changes were seen in schizophrenia.

Conclusions

Our anatomical data argue against prominent structural alterations of the habenular nuclei in schizophrenia but demonstrate robust alterations in depressive patients. We are currently applying immunohistochemical markers to better characterize neuronal subpopulations of this brain region in schizophrenia and depression.
Relationship between baseline white-matter changes and development of late-life depressive symptoms: 3-year results from the LADIS study
Authors: Teodorczuk A. , Firbank M. J. , Pantoni L. , Poggesi A. , Erkinjuntti T. , Wallin A. , Wahlund L.-O. , Scheltens P. , Waldemar G. , Schrotter G. , Ferro J. M. , Chabriat H. , Bazner H. , Visser M. , Inzitari D. , O'Brien J. T.
Published: August 2009

Background

Growing evidence suggests that cerebral white-matter changes and depressive symptoms are linked directly along the causal pathway. We investigated whether baseline severity of cerebral white-matter changes predict longer-term future depressive outcomes in a community sample of non-disabled older adults.

Method

In the Leukoaraiosis and Disability in the Elderly (LADIS) study, a longitudinal multi-centre pan-European study, 639 older subjects underwent baseline structural magnetic resonance imaging (MRI) and clinical assessments. Baseline severity of white-matter changes was quantified volumetrically. Depressive outcomes were assessed in terms of depressive episodes and depressive symptoms, as measured by the Geriatric Depression Scale (GDS). Subjects were clinically reassessed annually for up to 3 years. Regression models were constructed to determine whether baseline severity of white-matter changes predicted future depressive outcomes, after controlling for confounding factors.

Results

Baseline severity of white-matter changes independently predicted depressive symptoms at both 2 (p<0.001) and 3 years (p=0.015). Similarly, white-matter changes predicted incident depression (p=0.02). Over the study period the population became significantly more disabled (p<0.001). When regression models were adjusted to account for the influence of the prospective variable transition to disability, baseline severity of white-matter changes no longer predicted depressive symptoms at 3 years (p=0.09) or incident depression (p=0.08).

Conclusions

Our results support the vascular depression hypothesis and strongly implicate white-matter changes in the pathogenesis of late-life depression. Furthermore, the findings indicate that, over time, part of the relationship between white-matter changes and depression may be mediated by loss of functional activity.
Depressive symptoms in early pregnancy disrupt attentional processing of infant emotion
Authors: Pearson R. M. , Cooper R. M. , Penton-Voak I. S. , Lightman S. L. , Evans J.
Published: August 2009

Background

Growing evidence suggests that perinatal depression is associated with disrupted mother–infant interactions and poor infant outcomes. Antenatal depression may play a key role in this cycle by disrupting the development of a maternal response to infant stimuli. The current study therefore investigated the impact of depressive symptoms on the basic cognitive processing of infant stimuli at the beginning of pregnancy.

Method

A total of 101 women were recruited by community midwives and tested at an average gestation of 11 weeks. An established computerized paradigm measured women's ability to disengage attention from infant and adult faces displaying negative positive and neutral emotions. Depressive symptoms were measured using a computerized interview (the Clinical Interview Schedule).

Results

The effect of infant emotion on women's ability to disengage from infant faces was found to be influenced by depressive symptoms. Non-depressed pregnant women took longer to disengage attention from distressed compared with non-distressed infant faces. This bias was not, however, seen in women experiencing depressive symptoms. There was a difference of −53 (s.d.=0.7) ms (95% confidence interval −90 to −14, p=0.007) between those with and without depressive symptoms in this measure of attentional bias towards distressed infant faces.

Conclusions

Our results suggest that depressive symptoms are already associated with differential attentional processing of infant emotion at the very beginning of childbearing. The findings have potential implications for our understanding of the impact of depressive symptoms during pregnancy on the developing mother–infant relationship.
The interaction between perinatal factors and childhood abuse in the risk of developing anorexia nervosa
Authors: Favaro A. , Tenconi E. , Santonastaso P.
Published: August 2009

Background

Perinatal factors seem to be implicated in the pathogenesis of anorexia nervosa (AN) and may be involved in the programming of stress response systems in humans. Our aim was to explore one of the possible pathways to explain the association between perinatal complications and a psychiatric disorder. In particular, we tested the hypothesis that neonatal immaturity may confer an enhanced vulnerability to AN after exposure to a severe stressful event, such as childhood abuse.

Method

The sample was composed of subjects who took part in a prevalence study carried out on a representative sample of the general population and cases of AN referred to an out-patient specialist unit. All subjects (n=663) were born in the two obstetric wards of Padua Hospital between 1971 and 1979. We analysed data using both a case-control and a cohort design.

Results

We found that functional signs of neonatal dysmaturity, but not a low birthweight or prematurity, had a significant additive interaction with childhood abuse in determining the risk for this illness. In normal subjects, but not in subjects with AN, neonatal dysmaturity was associated with being small, short or thin for gestational age at birth.

Conclusions

The synergistic effect of neonatal dysmaturity and childhood abuse in increasing the risk for AN provides evidence for the hypothesis that a prenatal programming of stress response systems can result in an impairment of the individual's resilience to severe stressful events.
Brain anatomy and ageing in non-demented adults with Down's syndrome: anin vivoMRI study
Authors: Beacher F. , Daly E. , Simmons A. , Prasher V. , Morris R. , Robinson C. , Lovestone S. , Murphy K. , Murphy D. G. M.
Published: August 2009

Background

People with Down's syndrome (DS) are at high risk for developing dementia in middle age. The biological basis for this is unknown. It has been proposed that non-demented adults with DS may undergo accelerated brain ageing.

Method

We used volumetric magnetic resonance imaging (MRI) and manual tracing to compare brain anatomy and ageing in 39 non-demented adults with DS and 42 healthy controls.

Results

Individuals with DS had significant differences in brain anatomy. Furthermore, individuals with DS had a significantly greater age-related reduction in volume of frontal, temporal and parietal lobes, and a significantly greater age-related increase in volume of peripheral cerebrospinal fluid (CSF).

Conclusions

Non-demented adults with DS have differences in brain anatomy and ‘accelerated’ ageing of some brain regions. This may increase their risk for age-related cognitive decline and Alzheimer's disease (AD).
A POWERFUL TEST OF THE AUTOREGRESSIVE UNIT ROOT HYPOTHESIS BASED ON A TUNING PARAMETER FREE STATISTIC
Authors: Nielsen Morten Ørregaard
Published: August 2009

This paper presents a family of simple nonparametric unit root tests indexed by one parameter,d, and containing the Breitung (2002,Journal of Econometrics108, 342–363) test as the special cased= 1. It is shown that (a) each member of the family withd> 0 is consistent, (b) the asymptotic distribution depends ondand thus reflects the parameter chosen to implement the test, and (c) because the asymptotic distribution depends ondand the test remains consistent for alld> 0, it is possible to analyze the power of the test for different values ofd. The usual Phillips–Perron and Dickey–Fuller type tests are indexed by bandwidth, lag length, etc., but have none of these three properties.

It is shown that members of the family withd< 1 have higher asymptotic local power than the Breitung (2002) test, and whendis small the asymptotic local power of the proposed nonparametric test is relatively close to the parametric power envelope, particularly in the case with a linear time trend. Furthermore, generalized least squares (GLS) detrending is shown to improve power whendis small, which is not the case for the Breitung (2002) test. Simulations demonstrate that when applying a sieve bootstrap procedure, the proposed variance ratio test has very good size properties, with finite-sample power that is higher than that of the Breitung (2002) test and even rivals the (nearly) optimal parametric GLS detrended augmented Dickey–Fuller test with lag length chosen by an information criterion.
The effect of using an online-based course on the learning of grammar inductively and deductively
Authors: AbuSeileek Ali Farhan
Published: August 2009

This study aims at exploring the effectiveness of using an online-based course on the learning of sentence types inductively and deductively. To achieve this purpose, a computer-mediated course was designed. The sample of the study consists of four groups taught under four treatments of grammar: (1) with computer-based learning inductively, (2) with computer-based learning deductively, (3) with non-computer-based learning inductively, and (4) with non-computer-based learning deductively. A pre-test/post-test design (between-subject) is used to investigate the effect of two factors: method (computer-based learning vs. non-computer-based learning) and technique (induction vs. deduction) on the students’ learning of sentence types. The results reveal a new manner of enhancing grammar learning based on the level of language structure complexity. The computer-based learning method is found to be functional for more complex and elaborate structures, like the complex sentence and compound complex sentence, and more complicated grammar structures need to be taught by means of the deductive technique. None of the inductive and deductive techniques is reported to be more practical with simple grammar structures such as the simple sentence and compound sentence.
New competencies in a new era? Examining the impact of a teacher training project
Authors: Dooly Melinda
Published: August 2009

This article describes follow-up research aimed at exploring the long-term impact on participants of a teacher training course that integrated a variety of projects focusing on ICT use in language teaching. Internet in education is often promoted for its features that allow for new opportunities for constructivist approaches in the classroom. Nevertheless, this will not simply happen on its own. Teacher education must help shift students teachers’ pedagogical premise toward approaches that promote autonomous learning and collaborative problem-solving. Teacher training can highlight how this can be supported through ICT.

The article chronicles the first year following the closure of a teacher-training project, paying particular attention to current practices and perspectives of the primary and secondary education teachers involved. Data were gathered through questionnaires and semi-structured e-mail interviews, along with field notes and ongoing observation of participants’ current teaching environments in order to generate material for triangulation and contextual understanding of the data. The analysis of whether the project described herein has contributed to reducing the gap between the theoretical framework of teaching competences in telecollaboration and its transferral to teaching praxis is significant for future input on other training programmes.
Validity and Reliability of a French Version of the Metacognitions Questionnaire in a Nonclinical Population
Authors: Larøi Frank , Van der Linden Martial , d’Acremont Mathieu
Published: August 2009

We investigated the psychometric properties of a French translation of the Metacognitions Questionnaire (MCQ). 265 participants from the French-speaking population of Belgium completed the MCQ. Construct validity was assessed by means of a factor analysis, retaining 5 factors for oblique rotation. Most items loaded on appropriate factors. Confirmatory factor analysis was also conducted in order to assess construct validity and to test goodness of fit to the original 5-factor structure. This revealed that the 5-factor structure had an adequate fit. In general, results offer evidence that the present French version of the MCQ taps into similar metacognitive aspects and that it possesses adequate psychometric properties, comparable to those reported in the original validation study of the MCQ.
What Contributes to the (Im)Balanced Division of Family Work Between the Sexes?
Authors: Lothaller Harald , Mikula Gerold , Schoebi Dominik
Published: August 2009

This study examines a comprehensive set of variables proposed to explain the imbalance in the division of family work between the sexes. The analyses use survey data of 735 dual-earner couples from Austria, the Netherlands, and Portugal. The results support theoretical explanations that refer to time availability, gender ideology, relative resources, and the importance of characteristics of the family system. No support was obtained for the doing-gender perspective. Additional findings suggest that increased consideration of psychological concepts adds to the understanding of why women do more family work than men. The analyses revealed similarities, but also differences between the factors that contribute to the division of household labor and childcare.