bluuebunny/crossref_metadata_2025 huggingface dataset:
The Influence of Auditory Acuity on Acoustic Variability and the Use of Motor Equivalence During Adaptation to a Perturbation
Authors: Brunner Jana , Ghosh Satrajit , Hoole Philip , Matthies Melanie , Tiede Mark , Perkell Joseph
Published: October 2010

Purpose

The aim of this study was to relate speakers' auditory acuity for the sibilant contrast, their use of motor equivalent trading relationships in producing the sibilant /ʃ/, and their produced acoustic distance between the sibilants /s/ and /ʃ/. Specifically, the study tested the hypotheses that during adaptation to a perturbation of vocal-tract shape, high-acuity speakers use motor equivalence strategies to a greater extent than do low-acuity speakers in order to reach their smaller phonemic goal regions, and that high-acuity speakers produce greater acoustic distance between 2 sibilant phonemes than do low-acuity speakers.

Method

Articulographic data from 7 German speakers adapting to a perturbation were analyzed for the use of motor equivalence. The speakers' produced acoustic distance between /s/ and /ʃ/ was calculated. Auditory acuity was assessed for the same speakers.

Results

High-acuity speakers used motor equivalence to a greater extent when adapting to a perturbation than did low-acuity speakers. Additionally, high-acuity speakers produced greater acoustic contrasts than did low-acuity-speakers. It was observed that speech rate had an influence on the use of motor equivalence: Slow speakers used motor equivalence to a lesser degree than did fast speakers.

Conclusion

These results provide support for the mutual interdependence of speech perception and production.
Fast Mapping and Word Learning by Preschoolers With Specific Language Impairment in a Supported Learning Context: Effect of Encoding Cues, Phonotactic Probability, and Object Familiarity
Authors: Gray Shelley , Brinkley Shara
Published: October 2010

Purpose

To investigate whether phonological or semantic encoding cues improved the fast mapping or word learning performance of preschoolers with specific language impairment (SLI) or typical development (TD) and whether performance varied for words containing high- or low-frequency sublexical sequences that named familiar or unfamiliar objects.

Method

Forty-two preschoolers with SLI, 42 preschoolers with TD matched for age and gender to the children with SLI, and 41 preschoolers with TD matched for expressive vocabulary and gender to the children with SLI learned words in a supported learning context. Fast mapping, word learning, and post-task performance were assessed.

Results

Encoding cues had no effect on fast mapping performance for any group or on the number of words children learned to comprehend. Encoding cues appeared to be detrimental to word production for children with TD. Across groups, a clear learning advantage was observed for words with low-frequency sequences and, to a lesser extent, words associated with an unfamiliar object.

Conclusion

The results suggest that phonotactic probability and previous lexical knowledge affect word learning in similar ways for children with TD and SLI and that encoding cues were not beneficial for any group.
Rhythmic Versus Phonemic Interference in Delayed Auditory Feedback
Authors: Kaspar Kai , Rübeling Hartmut
Published: October 2010

Purpose

Delayed auditory feedback (DAF) of a speaker’s voice disturbs normal speech production. Various traditional theories assume that the content of the delayed feedback signal interferes with the actual production of a particular speech unit (
phonemic content hypothesis
). The
displaced rhythm hypothesis
as an alternative explanation suggests that speech disturbances arise from a disruptive rhythm that is produced by the delayed speech signal. The present experimental study directly contrasted the role of rhythm and speech content in a DAF task using speech units as stimuli.

Method

One hundred fifty-one participants read aloud 4 different sequences of double syllables that varied in phonemic content and rhythm while auditory feedback was either nondelayed or delayed by 200 or 400 ms.

Results

In line with previous studies, the authors found a peak of disturbances at a delay of about 200 ms, independent of speech rate. More important, the present results clearly support the displaced rhythm hypothesis. A speech rate dependency of this effect was also found.

Conclusion

Rhythm seems to be a significant criterion of speech monitoring, and hence a mismatch between spoken words and auditory feedback realized by DAF induces obvious speech problems on rhythmic level regardless of phonemic discrepancy at the same time.
Distributions of HLA‐DRB1/DQB1 alleles and haplotypes in the North‐eastern Thai population: indicative of a distinct Thai population with Chinese admixtures in the Central Thais
Authors: Romphruk A. V. , Puapairoj C. , Romphruk A. , Barasrux S. , Leelayuwat Y. Urwijitaroon* & C.
Published: October 2010

The phenotype and gene frequencies of HLA class II alleles were studied in the North‐eastern Thai population. Blood samples were collected from 100 unrelated healthy North‐eastern Thais. The HLA‐DRB1 and DQB1 genes were typed using the polymerase chain reaction – sequence specific primer (PCR‐SSP) and polymerase chain reaction – sequence specific oligonucleotide probe (PCR‐SSO) techniques. Twenty‐six HLA‐DRB1 and 11 DQB1 alleles were found in this population. DRB1*1202, 1502, 0405 and DQB1*0502/0504, 0301/0304 alleles were commonly found. Linkage disequilibrium analysis suggested the existence of 13 DR‐DQ haplotypes. The DRB1*1502‐DQB1*0501 haplotype was the most common. The DRB1*1106‐DQB1*0301/0304 haplotype was found only in North‐eastern Thais and not in other Thai populations. Comparative analysis of the HLA‐DR/DQ alleles revealed differences in the distributions of these alleles amongst different ethnic groups. Interestingly, the distributions of HLA class II alleles in Central Thai, North‐eastern Thai and Southern Chinese populations are similar. However, it appears that the distribution in the Central Thais is a mixture of those in Southern Chinese and North‐eastern Thais, suggesting the existence of Thai–Chinese admixtures in the Central Thai population. This study provides basic information for further studies of the MHC in anthropology, organ transplantation and disease susceptibility in the North‐eastern Thai population.
Phylogenetic analysis of primate MIC (PERB11) sequences suggests that the representation of the gene family differs in different primates: comparison of MIC (PERB11) and C4
Authors: Cattley S. K. , Longman N. , Dawkins R. L. , Gaudieri S. , Kulski J. K. , Leelayuwat C.
Published: October 2010

Duplication of segments within the MHC has led to numerous multicopy families such as class I, class II, C4 and MIC (PERB11). Different copy numbers between haplotypes and species may be explained by the extent of duplication and subsequent deletion. There are at least five copies of MIC (PERB11) in humans, but MICA (PERB11.1) appears to have been deleted from the chimpanzee.

By comparing the sequences of primates (chimpanzee, gorilla, gibbon, orang‐utan, pygmy chimpanzee, Patas monkey, Aethiops and baboon) we conclude that the gorilla has a copy of PERB11.1, whereas the baboon and Patas possess MICD (PERB11.4) and/or MICE (PERB11.5) rather than MICA (PERB11.1). These findings indicate that the primate MHC is more plastic than has been appreciated.
‘Ah Famous Citie’: Women, Writing, and Early Modern London
Authors: Wilcox Helen
Published: October 2010

This article explores aspects of the textual relationship between women and early modern London by examining three verbal ‘snapshots’ of the city in works either written by women or focusing on women in their urban environment. The first text, Isabella Whitney's ‘Wyll and Testament’ (1573), addresses London from a rural perspective, treating the city as a fickle male to whom she wants to hand back all his treasures. The poem constructs a vivid and ironic social topography, giving a glimpse of the roles of men and women in the Tudor city. The second text is by Mary Carleton, the roguish Restoration figure who defended her apparently ‘counterfeit’ life in the prose of The Case of Madam Mary Carleton (1663). Carleton's London is a place of unwanted seduction and sexual intimidation, highlighting a gendered moral geography even while the memoir itself titillates the reader with the account of her bizarre experiences. Finally, in a coda to the discussions of Whitney and Carleton, early eighteenth-century London is viewed through Jonathan Swift's satirical mock-pastorals of squalid urban life, in which female identity, like the city itself, is a site of violence, disgust and deception. Together, these textual representations of women and early modern London indicate the complex interactions of gender, literature and the early modern city. The analysis of the texts also suggests the significance of the ironic voice as a quintessentially urban literary mode, the prevalence of the idea of woman as a commodified topographical site, and the function of metaphors of courtship or marriage as indicators of the paradoxical attractions of the city.
Revolutionary Voices: Nordic Women Writers and the Development of Female Urban Prose 1860–1900
Authors: Klok Janke
Published: October 2010

In 1795, Mary Wollstonecraft's travels to Scandinavian cities gave her new perspectives on the English and Continental bourgeois cultures with which she was acquainted. Her notions of the city as a source of inspiration for self-knowledge and knowledge of the world are echoed in the epistolary writings of the Norwegian author Camilla Collett (1813–1895) and the novels of her countrywoman Amalie Skram (1846–1905). Collett and Skram were both frequent visitors to different European capital cities, and incorporated their impressions and experiences of these cities. This resulted in innovative texts, with the individual in a new, modern environment, the city, as one of the central themes. For Collett, who can be regarded as a city correspondent avant la lettre, the city was also a yardstick for cultural progress. In her novels, Skram used the European city as a sort of laboratory of the modern era. Nevertheless, Collett's and Skram's ‘city texts’ are not the ones that have ensured that these two authors found their way into the literary canon. Collett became famous as the author of the first Norwegian feminist novel, whereas Skram is known as a Norwegian naturalist. Until recently, the prose texts in which Collett and Skram processed their urban experiences were either not discussed in Norwegian literary historiography, or were labelled as contributions to the morality debate that raged in Scandinavia at the end of the nineteenth century. In this article, I shall propose that Collett and Skram contribute to a distinctive yet unrecognized genre – female urban prose – which proffers new modes of thinking and writing about women's experience of contemporaneous bourgeois culture.
Playing for All in the City: Women's Drama
Authors: Findlay Alison
Published: October 2010

English women's drama was crucially shaped by the city between 1660 and 1705, the period when female actors and playwrights first entered the professional theatre. This article uses selected scenes from the comedies of Elizabeth Polwhele, Aphra Behn and Susanna Centlivre to examine how women coped with the high-risk strategy of participating in commercial theatre and the vast circulation of trade which grew up around the City, a flamboyant sign of high capitalism. On one hand, the city represents movement, a crossroads of possibilities in which to redefine female agency. In plays such as The Rover, The Frolicks and The Gamester, female dramatists script movement across the city in a way that pre-empts De Certeau's model of ‘walking the city’ as a way for female characters and actors to inhabit public spaces of their own. On the other hand, scenes in these plays critically interrogate Raymond Williams’ classic distinction between discursive constructions of the city and the countryside in which the city's blatant expose of social and economic processes is associated with dirt. The contaminating pollution is feminised in the trope of actress, playwright and whore. Actresses and playwrights were ‘playing for all’ in more than one sense, and gambling exemplifies the risks involved for women attempting to manipulate the urban and theatrical locations that attempted to commodify them.
Queer Sex in the Metropolis? Place, Subjectivity and the Second World War
Authors: Vickers Emma
Published: October 2010

The strong links between cities and queer culture and its expression have occupied numerous scholars, including Henning Bech and Matt Houlbrook. Indeed, London has been viewed as a focal point of British queer urban culture for over 200 years and, as this article demonstrates, the advent of the Second World War did not preclude this centrality but ensured that the city became a focal point for service personnel on leave. Yet, the emphasis placed on the metropolises in analysing space and queer expression has rendered invisible the use of more transient spaces outside of the city. This article seeks to examine these ‘alternative’ or opportunistic sites of expression, using oral testimony from queer men who served with the British Armed Forces during the Second World War. The memories of these servicemen and the significance they place on space/locations demonstrate the need to engage with subjective sites or ‘geographies’ of queerness both inside and outside of the city between 1939 and 1945.
Orientational dynamics of water trapped between two nanoscopic hydrophobic solutes: A molecular dynamics simulation study
Authors: Choudhury Niharendu
Published: October 2010

We investigate thoroughly the effect of confinement and solute topology on the orientational dynamics of water molecule in the interplate region between two nanoscopic hydrophobic paraffinlike plates. Results are obtained from molecular dynamics simulations of aqueous solutions of paraffinlike plates in the isothermal-isobaric ensemble. An analysis of survival time auto correlation function shows that the residence time of the water molecule in the confined region between two model nanoscopic hydrophobic plates depends on solute surface topology (intermolecular distance within the paraffinlike plate). As expected, the extent of confinement also changes the residence time of water molecules considerably. Orientational dynamics was analyzed along three different directions, viz., dipole moment, HH, and perpendicular to molecular plane vectors. It has been demonstrated that the rotational dynamics of the confined water does not follow the Debye rotational diffusion model, and surface topology of the solute plate and the extent of confinement have considerable effect on the rotational dynamics of the confined water molecules.
A self-consistent Ornstein–Zernike approximation for a fluid with a screened power series interaction
Authors: Yasutomi M.
Published: October 2010

We present a thermodynamically self-consistent Ornstein–Zernike approximation (SCOZA) for a fluid of spherical particles with a pair potential given by a hard-core repulsion and screened power series (SPS) tails. We take advantage of the known analytic properties of the solution of the Ornstein–Zernike equation for the case in which the direct correlation function outside the repulsive core is given by the SPS tails [M. Yasutomi, J. Phys.: Condens. Matter 13, L255 (2001)]: c(r)=∑n=1Nexp(−znr)∑τ=−1LnK(n,τ)znτ+1rτ  r>1. The analytic properties are rewritten so as to be optimally suited to the numerical computations. The SCOZA is known to provide very good overall thermodynamics, remarkably accurate critical point, and coexistence curve. In this paper, we present some numerical results for parameters in c(r) which are chosen to fit the Lennard-Jones potential. We show that both the energy and the compressibility paths lead to the same thermodynamics with high accuracy due to the thermodynamic consistency condition that has been enforced. The present method will be applicable to fluids with a large variety of smooth, realistic isotropic potentials where the pair potentials can be fitted by the SPS tails. The fitting procedure is superior to that by multi-Yukawa tails which is the only method presented so far.
Fragmentation patterns of core-ionized thymine and 5-bromouracil
Authors: Itälä E. , Ha D. T. , Kooser K. , Rachlew E. , Huels M. A. , Kukk E.
Published: October 2010

Photofragmentation of thymine and 5-bromouracil into cation and neutral fragments following the core ionization by soft x-rays using photoelectron-photoion-photoion coincidence technique has been studied. The fragment ion mass spectra were recorded in coincidence with the C 1s photoelectron spectra. In the case of thymine, deuterated samples were used to identify fragments. Deuteration or bromination allowed us to study not only the main fragmentation channels of these pyrimidine bases, but also to investigate if replacement of an exocyclic functional group affects molecular fragmentation. We found that the dominant fragmentation channels involve only one starting geometry, and the base ring and other bond cleavages, leading to the detected fragments, are essentially identical between thymine and 5-bromouracil. In addition, the relative intensities of the strongest fragmentation channels were determined and compared with calculated appearance energies using ab initio unrestricted Hartree–Fock theory.
Heterogeneous dynamics in columnar liquid crystals of parallel hard rods
Authors: Belli Simone , Patti Alessandro , van Roij René , Dijkstra Marjolein
Published: October 2010

In the wake of previous studies on the rattling-and-jumping diffusion in smectic liquid crystal phases of colloidal rods, we analyze here for the first time the heterogeneous dynamics in columnar phases. More specifically, we perform computer simulations to investigate the relaxation dynamics of a binary mixture of perfectly aligned hard spherocylinders. We detect that the columnar arrangement of the system produces free-energy barriers that the particles should overcome to jump from one column to another, thus determining a hopping-type diffusion. This phenomenon accounts for the non-Gaussian intercolumn diffusion and shows a two-step structural relaxation that is remarkably analogous to that of out-of-equilibrium glass-forming systems and gels. Surprisingly enough, slight deviations from the behavior of simple liquids due to transient cages is also observed in the direction perpendicular to this plane, where the system is usually referred to as liquidlike.
The Neighbourhood Effects of New Immigration
Authors: Robinson David
Published: October 2010

Since the early 1990s global migration flows have become larger in scale and more varied in form. In the UK, controversy has surrounded this new phase of migration and it has often been assumed to be having a detrimental affect on the well-being of settled residents. Yet, there is dearth of information about the impacts of new immigration and what evidence does exist is curiously place-less, making it difficult to say anything about local effects. This paper is an attempt to fill this gap in understanding by outlining a framework to support the exploration of neighbourhood effects of new immigration. At its heart lies a commitment to three types of explanation for geographical variations in local experiences of new immigration: the individuals living in a place; the opportunity structures apparent in the local environment; and the sociocultural features of local communities.
Evolution along the crassulacean acid metabolism continuum
Authors: Silvera Katia , Neubig Kurt M. , Whitten W. Mark , Williams Norris H. , Winter Klaus , Cushman John C.
Published: October 2010

Crassulacean acid metabolism (CAM) is a specialised mode of photosynthesis that improves atmospheric CO2 assimilation in water-limited terrestrial and epiphytic habitats and in CO2-limited aquatic environments. In contrast with C3 and C4 plants, CAM plants take up CO2 from the atmosphere partially or predominantly at night. CAM is taxonomically widespread among vascular plants and is present in many succulent species that occupy semiarid regions, as well as in tropical epiphytes and in some aquatic macrophytes. This water-conserving photosynthetic pathway has evolved multiple times and is found in close to 6% of vascular plant species from at least 35 families. Although many aspects of CAM molecular biology, biochemistry and ecophysiology are well understood, relatively little is known about the evolutionary origins of CAM. This review focuses on five main topics: (1) the permutations and plasticity of CAM, (2) the requirements for CAM evolution, (3) the drivers of CAM evolution, (4) the prevalence and taxonomic distribution of CAM among vascular plants with emphasis on the Orchidaceae and (5) the molecular underpinnings of CAM evolution including circadian clock regulation of gene expression.
Ethylene production under high temperature stress causes premature leaf senescence in soybean
Authors: Djanaguiraman Maduraimuthu , Prasad P. V. Vara
Published: October 2010

Leaf senescence in soybean (Glycine max L. Merr.) occurs during the later stages of reproductive development and can be triggered or enhanced by high temperature (HT) stress. Ethylene production can trigger premature leaf senescence, but it is unclear whether HT stress produces ethylene and the subsequent influence on physiology and yield of soybean is also uncertain. We hypothesised that ethylene produced under HT stress is involved in premature leaf senescence and that use of an ethylene perception inhibitor would influence physiology and yield. Objectives of this study were to (1) quantify HT-stress-induced ethylene production; (2) quantify effects of HT stress and application of an ethylene perception inhibitor (1-methylcyclopropene; 1-MCP) on source strength traits such as photosynthetic rate, oxidant production, membrane damage and sugar accumulation; and (3) evaluate efficacy of 1-MCP on minimising HT-stress-induced effects on physiological and yield traits. Soybean plants were exposed to HT (38/28°C) or optimum temperature (OT, 28/18°C) for 14 days at the beginning of pod set. Plants at each temperature were treated with 1 μg L–1 1-MCP or left untreated (control). HT stress enhanced ethylene production rates in leaves and pods by 3.2- and 2.1-fold over OT. HT stress decreased photochemical efficiency (5.8%), photosynthetic rate (12.7%), sucrose content (21.5%), superoxide dismutase (13.3%), catalase (44.6%) and peroxidase (42.9%) enzymes activity and increased superoxide radical (63%) and hydrogen peroxide (70.4%) content and membrane damage (54.7%) compared with OT. Application of 1-MCP decreased ethylene production rate and premature leaf senescence traits by enhancing the antioxidant defence system. HT stress decreased seed set percentage (18.6%), seed size (64.5%) and seed yield plant–1 (71.4%) compared with OT, however, foliar spray of 1-MCP increased the seed set percent and seed size, which resulted in a higher yield than the unsprayed control. The present study showed HT stress increased ethylene production rate, which triggered premature leaf senescence, whereas 1-MCP application reduced or postponed premature leaf senescence traits by inhibiting ethylene production.
Shoot architecture, growth and development dynamics of Vitis vinifera cv. Semillon vines grown in an irrigated vineyard with and without shade covering
Authors: Greer Dennis H. , Weston Chris , Weedon Mark
Published: October 2010

Covering vines with shade cloth has been proposed as a means of reducing canopy temperatures to reduce heat impacts. Because shade cloth concomitantly reduces irradiance, the objective of the study was to assess the effects of shade covering on growth and development of Semillon (Vitis vinifera L.) vines in vineyard conditions over three growing seasons. Air and canopy temperatures were measured throughout. Stem extension and leaf areas were measured on selected shoots throughout the season and at harvest, all shoots were destructively harvested and internode lengths, leaf areas and stem lengths were measured and leaves, stems and bunches dried to the determine the dry matter of each shoot. Results showed shoot growth, architecture and development were all affected by the shade. Total shoot biomass was reduced by 20%, although shoot biomass allocation was not affected. The distribution of different shoot types, based on numbers of nodes and stem lengths, was shifted in favour of medium length shoots at the expense of long shoots under the shade, consistent with decreased apical meristem activity in shade conditions. Shade also caused a major impediment to leaf development, with individual leaves delayed in expansion by 10–25 days compared with leaves on exposed vines at comparable stages of development. However, the delay in development was offset by expansion; shaded leaves expanding to a larger size than for exposed leaves. The difference in leaf size may be a strategy to compensate for the slower development in the shade conditions.
Examination of pre-industrial and future [CO2] reveals the temperature-dependent CO2 sensitivity of light energy partitioning at PSII in eucalypts
Authors: Logan Barry A. , Hricko Carolyn R. , Lewis James D. , Ghannoum Oula , Phillips Nathan G. , Smith Renee , Conroy Jann P. , Tissue David T.
Published: October 2010

We grew faster-growing Eucalyptus saligna Sm. and slower-growing Eucalyptus sideroxylon A. Cunn ex Woolls tree seedlings in sunlit glasshouses at all combinations of 290 µL L–1 (pre-industrial), 400 µL L–1 (modern) or 650 µL L–1 (future) global atmospheric CO2 ([CO2]), and ambient or ambient + 4°C temperature. To assess photosynthetic performance, we simultaneously measured light-saturated CO2 assimilation (Asat) and chlorophyll fluorescence emission along with the capacity for photosynthetic O2 evolution and leaf pigment composition. Photosynthetic response to [CO2] was similar between species. Increasing [CO2] but not temperature increased Asat. The response of photosynthetic electron transport to [CO2] was temperature-dependent and manifested through adjustments in energy partitioning at PSII. Increasing [CO2] resulted in greater PSII operating efficiencies at the elevated temperature. We observed no associated acclimatory adjustments in the capacity for photosynthetic O2 evolution or changes in leaf chlorophyll content. Photoprotective energy dissipation responded to increasing [CO2] and temperature. Across species and treatments, increased energy partitioning to electron transport was always associated with decreased partitioning to energy dissipation. Our results suggest that in response to increasing [CO2] and temperature, E. saligna and E. sideroxylon meet increased demands for the products of electron transport via adjustments in energy partitioning, not through acclimation of the capacity for photosynthetic electron transport or light absorption.
Host-free, yellow phosphorescent material in white organic light-emitting diodes
Authors: Lee Meng-Ting , Chu Miao-Tsai , Lin Jin-Sheng , Tseng Mei-Rurng
Published: October 2010

A white organic light-emitting diode (WOLED) with a high power efficiency has been demonstrated by dispersing a host-free, yellow phosphorescent material in between double blue phosphorescent emitters. The device performance achieved a comparable value to that of using a complicated host–guest doping system to form the yellow emitter in WOLEDs. Based on this device concept as well as the molecular engineering of blue phosphorescent host material and light-extraction film, a WOLED with a power efficiency of 65 lm W−1at a practical brightness of 1000 cd m−2with Commission Internationale d'Echariage coordinates (CIEx,y) of (0.37, 0.47) was achieved.
Ac-driven plasma torch with a well-type cathode working in air and CO2
Authors: Hur M , Kim K T , Song Y H
Published: October 2010

This work is devoted to the investigation of the discharge characteristics of an ac arc plasma torch with a well-type cathode working in air and CO2. The electrical characteristics, plasma jet image and optical emission profile are investigated by varying the discharge power and the gas flow rate. The dynamic behaviour of arc voltage and current is characterized by smooth-shaped waveforms, regularly iterated with a driving frequency. The moving of arc spot positions is inferred from the measured waveforms, and compared with that observed in dc torches. A simple lifetime test is performed to verify the speculation that the arc spots in ac operation move continuously over a wide region with a very high speed. The result shows that the electrode lifetime can be enhanced by combining the vortex motion of arc gas with the ac driving.
R/qtl: high-throughput multiple QTL mapping
Authors: Arends Danny , Prins Pjotr , Jansen Ritsert C. , Broman Karl W.
Published: October 2010

Motivation: R/qtl is free and powerful software for mapping and exploring quantitative trait loci (QTL). R/qtl provides a fully comprehensive range of methods for a wide range of experimental cross types. We recently added multiple QTL mapping (MQM) to R/qtl. MQM adds higher statistical power to detect and disentangle the effects of multiple linked and unlinked QTL compared with many other methods. MQM for R/qtl adds many new features including improved handling of missing data, analysis of 10 000 s of molecular traits, permutation for determining significance thresholds for QTL and QTL hot spots, and visualizations for cis–trans and QTL interaction effects. MQM for R/qtl is the first free and open source implementation of MQM that is multi-platform, scalable and suitable for automated procedures and large genetical genomics datasets.

Availability: R/qtl is free and open source multi-platform software for the statistical language R, and is made available under the GPLv3 license. R/qtl can be installed from http://www.rqtl.org/. R/qtl queries should be directed at the mailing list, see http://www.rqtl.org/list/.

Contact:  kbroman@biostat.wisc.edu
Urinary 8‐hydroxy‐2′‐deoxyguanosine reflects symptomatic status and severity of systolic dysfunction in patients with chronic heart failure
Authors: Kobayashi Shigeki , Susa Takehisa , Tanaka Takeo , Wada Yasuaki , Okuda Shinichi , Doi Masahiro , Nao Tomoko , Yoshiga Yasuhiro , Yamada Jutaro , Okamura Takayuki , Ueyama Takeshi , Kawamura Syuji , Yano Masafumi , Matsuzaki Masunori
Published: October 2010

Aims

Oxidative stress is known to play a crucial role in the pathogenesis of heart failure (HF). We investigated whether urinary 8‐hydroxy‐2′‐deoxyguanosine (8‐OHdG), a product of oxidative DNA damage, is a clinically useful biomarker of the severity of chronic heart failure (CHF) and oxidative stress levels in failing hearts.

Methods and results

We measured 8‐OHdG in the serum obtained from the coronary sinus (CS) and aortic root (Ao) in small groups of control subjects and CHF patients. We then measured urinary 8‐OHdG and other biomarkers (brain natriuretic peptide, 8‐isoplastane, high‐sensitivity C‐reactive protein, interleukin‐6, and tumour necrosis factor‐α) in 31 control subjects and 194 patients with CHF [left‐ventricular ejection fraction (LVEF): 28.3 ± 8.1%]. Serum 8‐OHdG was significantly higher in the CS than the Ao in CHF patients only. Urinary 8‐OHdG was also significantly higher in CHF patients than in control subjects, and urinary 8‐OHdG became higher as New York Heart Association class increased. Moreover, there was a significant correlation between urinary 8‐OHdG and LVEF (r = −0.27), pulmonary capillary wedge pressure (r = 0.31), or left‐ventricular end‐diastolic volume index (r = 0.22). In contrast, there was poor correlation between the severity of CHF and the other neurohumoral biomarkers.

Conclusion

In HF, urinary 8‐OHdG seems to reflect the level of oxidative stress and various parameters related to symptomatic status and functional severity of CHF.
Salivary Gland Disorders
Authors: Hasan Sofia , Khan Taimur
Published: October 2010

Salivary gland disease represents a relatively minor proportion of a GP workload. On average, a GP will see a new case of head and neck cancer every 6 years. Early recognition and referral improves outcomes. This article aims to explain common salivary gland pathologies and their management, including the recognition and management of benign and malignant salivary neoplasms.
Adult Hip Pain
Authors: Cundall-Curry Duncan
Published: October 2010

Hip pain can affect patients of all ages with vastly differing presentations. Presentation may be acute or insidious, and the patient may present with limp, immobility or no functional disturbance. Pain in the hip can also be misleading due to referred pain from the lumbar spine, abdomen, pelvis or knee.
Eligibility for Free Health Care
Authors: Edwards Duncan , Marcus Rebecca
Published: October 2010

The regulations determining eligibility for free health care in the UK have become increasingly complex and politically contested at a time of increased international migration. Eligibility for free health care in the UK is determined by the residency status of an individual and not by nationality or taxation status.
Hearing Loss
Authors: Barden Sarah , Simon Chantal , Jones Nick
Published: October 2010

In the UK, there are 9 million people who are deaf or hard of hearing and potentially facing significant communication barriers. Hearing loss can be broadly divided into two main types—conductive and sensorineural. The former is usually caused by pathology within the external or middle ear, the latter by inner ear disease (the cochlea or neural pathway to the auditory cortex). A patient can also have a mixed picture with both conductive and sensorineural elements. This article describes the initial assessment and investigation of a patient presenting with hearing loss, outlines the more common causes of both conductive and sensorineural deafness and outlines strategies to optimize hearing.
Theory Driven Bias in Ideal Point Estimates—A Monte Carlo Study
Authors: Hirsch Alexander V.
Published: October 2010

This paper analyzes the use of ideal point estimates for testing pivot theories of lawmaking such as Krehbiel's (1998, Pivotal politics: A theory of U.S. lawmaking. Chicago, IL: University of Chicago) pivotal politics and Cox and McCubbins's (2005, Setting the Agenda: Responsible Party Government in the U.S. House of Representations. New York: Cambridge University Press) party cartel model. Among the prediction of pivot theories is that all pivotal legislators will vote identically on all successful legislation. Clinton (2007, Lawmaking and roll calls. Journal of Politics 69:455–67) argues that the estimated ideal points of the pivotal legislators are therefore predicted to be statistically indistinguishable and false when estimated from the set of successful final passage roll call votes, which implies that ideal point estimates cannot logically be used to test pivot theories. I show using Monte Carlo simulation that when pivot theories are augmented with probabilistic voting, Clinton's prediction only holds in small samples when voting is near perfect. I furthermore show that the predicted bias is unlikely to be consequential with U.S. Congressional voting data. My analysis suggests that the methodology of estimating ideal points to compute theoretically relevant quantities for empirical tests is not inherently flawed in the case of pivot theories.
Cow's‐Milk Allergy Is a Risk Factor for the Development of FGIDs in Children
Authors: Saps Miguel , Lu Peter , Bonilla Silvana
Published: October 2010

Objectives:

Functional gastrointestinal disorders (FGIDs) are common in children. Their pathogenesis remains unknown and is most likely multifactorial. We hypothesized that noninfectious causes of inflammation affecting the gastrointestinal (GI) tract early in life, such as cow's‐milk allergy (CMA), can predispose to the development of FGIDs later in childhood.

Patients and Methods:

Case‐control study. Subjects were patients between 4 and 18 years diagnosed with CMA in the first year of life at Children's Memorial Hospital in Chicago, IL, between January 2000 and June 2009. Diagnosis of CMA was based on history and clinical findings. Siblings 4 to 18 years of age without a history of CMA were selected as controls. Cases completed the parental form of the Pediatric Gastrointestinal Symptoms Rome III version questionnaire to assess for GI symptoms.

Results:

Fifty‐two subjects (mean age 8.1 ± 4.48 years, 62% girls) and 53 controls (mean age 9.7 ± 4.20 years, 55% girls) participated in the study. Twenty‐three of 52 subjects (44.2%) reported GI symptoms that included abdominal pain, constipation, or diarrhea compared with 11 of 53 controls (20.75%) (odds ratio 3.03, P = 0.01). Abdominal pain was significantly more common in cases (16/52, 30.8%) versus controls (5/53, 9.43%) (odds ratio 4.27 [1.43–12.7]) (χ2 = 7.47, P = 0.01). Abnormal stool habits were more common in cases (15/52, 28.8%) versus controls (7/53, 13.2%), but the difference was not statistically significant. Ten of 52 subjects (19.2%) met the Questionnaire on Pediatric Gastrointestinal Symptoms Rome III version criteria for diagnosis of an FGID (7 irritable bowel syndrome, 2 functional dyspepsia, 1 functional abdominal pain), whereas none in the control group did.

Conclusions:

CMA constitutes a risk factor for the development of FGIDs in children.
Effect of frameshift mutagen acriflavine on control of resistance genes in Acinetobacter baumannii
Authors: Lopes B. S. , Hamouda A. , Findlay J. , Amyes S. G. B.
Published: October 2010

Acinetobacter baumannii is a Gram-negative pathogenic bacterium that often exhibits a multidrug-resistant phenotype causing infections at various sites of the body and increasingly leading to septicaemic shock. This study evaluated the role of acriflavine, a frameshift mutagen, on the movement of insertion sequence ISAba1 in clinical isolates of A. baumannii, with the focus on changes in expression levels of the bla
ADC and bla
OXA-51-like genes. Resistance profiles were assessed with consideration of ISAba1 acting as a promoter upstream of the bla
ADC or bla
OXA-51-like gene. ISAba1 movement was observed in the acriflavine mutants Ab153M and Ab1225M. Ab153M exhibited an increase in the MIC values of carbapenems and ceftazidime, with ISAba1 gained upstream of the bla
ADC and bla
OXA-51-like genes, correlating with an increase in gene expression. Reduced expression of the 17, 23 and 25 kDa outer-membrane proteins (OMPs) was also observed in Ab153M. There was a significant decrease in MIC values of carbapenems with the loss of ISAba1 upstream of the bla
ADC and bla
OXA-51-like genes in strain Ab1225M, and a significant decrease in bla
OXA-51-like gene expression and, to a lesser extent, in bla
ADC expression. Ab1225M and a serially subcultured Ab1225 strain (Ab1225s) exhibited overexpression of the 17, 23, 25 and 27 kDa OMPs. There was a decrease in MIC values of the carbapenems and piperacillin/tazobactam but not of ceftazidime in Ab1225s, which had ISAba1 upstream of the bla
ADC and bla
OXA-51-like genes. A significant decrease in bla
OXA-51-like expression was observed in Ab1225s, whereas the expression of bla
ADC was similar to that in the Ab1225 parental strain. The attenuation in this strain may be due to overexpression of OMPs and it is clear that, even if ISAba1 is present upstream of an antibiotic resistance gene, it may not necessarily contribute towards the overexpression of antibiotic resistance genes (bla
OXA-51-like in Ab1225s). Movement of the IS element within the A. baumannii chromosome may be an important regulatory mechanism employed by the bacterium under particular stress conditions, and the ability to upregulate the expression of antibiotic resistance genes is likely to be an important factor in the pathogenicity of this bacterium.
Escherichia coli mhpR gene expression is regulated by catabolite repression mediated by the cAMP–CRP complex
Authors: Manso I. , García J. L. , Galán B.
Published: October 2010

The expression of themhpgenes involved in the degradation of the aromatic compound 3-(3-hydroxyphenyl)propionic acid (3HPP) inEscherichia coliis dependent on the MhpR transcriptional activator at thePapromoter. This catabolic promoter is also subject to catabolic repression in the presence of glucose mediated by the cAMP–CRP complex. ThePrpromoter drives the MhpR-independent expression of the regulatory gene.In vivoandin vitroexperiments have shown that transcription from thePrpromoter is downregulated by the addition of glucose and this catabolic repression is also mediated by the cAMP–CRP complex. The activation role of the cAMP–CRP regulatory system was further investigated by DNase I footprinting assays, which showed that the cAMP–CRP complex binds to thePrpromoter sequence, protecting a region centred at position −40.5, which allowed the classification ofPras a class II CRP-dependent promoter. Open complex formation at thePrpromoter is observed only when RNA polymerase and cAMP–CRP are present. Finally, byin vitrotranscription assays we have demonstrated the absolute requirement of the cAMP–CRP complex for the activation of thePrpromoter.
AbaA and WetA govern distinct stages of Aspergillus fumigatus development
Authors: Tao Li , Yu Jae-Hyuk
Published: October 2010

The opportunistic human pathogenAspergillus fumigatusproduces a massive number of asexual spores (conidia) as the primary means of dispersal, survival, genome protection and infection of hosts. In this report, we investigate the functions of two developmental regulators,AfuAbaA andAfuWetA, inA. fumigatus. TheAfuabaAgene is predicted to encode an ATTS/TEA DNA-binding domain protein and is activated byAfuBrlA during the middle stage ofA. fumigatusasexual development (conidiation). The deletion ofAfuabaAresults in the formation of aberrant conidiophores exhibiting reiterated cylinder-like terminal cells lacking spores. Furthermore, the absence ofAfuabaAcauses delayed autolysis and cell death, whereas the overexpression ofAfuabaAaccelerates these processes, indicating an additional role forAfuAbaA. TheAfuwetAgene is sequentially activated byAfuAbaA in the late phase of conidiation. The deletion ofAfuwetAcauses the formation of defective spore walls and a lack of trehalose biogenesis, leading to a rapid loss of spore viability and reduced tolerance to various stresses. This is the first report to demonstrate that WetA is essential for trehalose biogenesis in conidia. Moreover, the absence ofAfuwetAcauses delayed germ-tube formation and reduced hyphal branching, suggesting a role ofAfuWetA in the early phase of fungal growth. A genetic model depicting the regulation of conidiation inA. fumigatusis proposed.
The pobA gene of Burkholderia cenocepacia encodes a Group I Sfp-type phosphopantetheinyltransferase required for biosynthesis of the siderophores ornibactin and pyochelin
Authors: Asghar Atif H. , Shastri Sravanthi , Dave Emma , Wowk Irena , Agnoli Kirsty , Cook Anne M. , Thomas Mark S.
Published: October 2010

The opportunistic pathogen Burkholderia cenocepacia produces the siderophores ornibactin and pyochelin under iron-restricted conditions. Biosynthesis of both siderophores requires the involvement of non-ribosomal peptide synthetases (NRPSs). Using a transposon containing the lacZ reporter gene, two B. cenocepacia mutants were isolated which were deficient in siderophore production. Mutant IW10 was shown to produce normal amounts of ornibactin but only trace amounts of pyochelin, whereas synthesis of both siderophores was abolished in AHA27. Growth of AHA27, but not IW10, was inhibited under iron-restricted conditions. In both mutants, the transposon had integrated into the pobA gene, which encodes a polypeptide exhibiting similarity to the Sfp-type phosphopantetheinyltransferases (PPTases). These enzymes are responsible for activation of NRPSs by the covalent attachment of the 4′-phosphopantetheine (P-pant) moiety of coenzyme A. Previously characterized PPTase genes from other bacteria were shown to efficiently complement both mutants for siderophore production when provided in trans. The B. cenocepacia pobA gene was also able to efficiently complement an Escherichia coli entD mutant for production of the siderophore enterobactin. Using mutant IW10, in which the lacZ gene carried by the transposon is inserted in the same orientation as pobA, it was shown that pobA is not appreciably iron-regulated. Finally, we confirmed that Sfp-type bacterial PPTases can be subdivided into two distinct groups, and we present the amino acid signature sequences which characterize each of these groups.
Variation in a surface-exposed region of the Mycoplasma pneumoniae P40 protein as a consequence of homologous DNA recombination between RepMP5 elements
Authors: Spuesens Emiel B. M. , van de Kreeke Nick , Estevão Silvia , Hoogenboezem Theo , Sluijter Marcel , Hartwig Nico G. , van Rossum Annemarie M. C. , Vink Cornelis
Published: October 2010

Mycoplasma pneumoniae is a human pathogen that causes a range of respiratory tract infections. The first step in infection is adherence of the bacteria to the respiratory epithelium. This step is mediated by a specialized organelle, which contains several proteins (cytadhesins) that have an important function in adherence. Two of these cytadhesins, P40 and P90, represent the proteolytic products from a single 130 kDa protein precursor, which is encoded by the MPN142 gene. Interestingly, MPN142 contains a repetitive DNA element, termed RepMP5, of which homologues are found at seven other loci within the M. pneumoniae genome. It has been hypothesized that these RepMP5 elements, which are similar but not identical in sequence, recombine with their counterpart within MPN142 and thereby provide a source of sequence variation for this gene. As this variation may give rise to amino acid changes within P40 and P90, the recombination between RepMP5 elements may constitute the basis of antigenic variation and, possibly, immune evasion by M. pneumoniae. To investigate the sequence variation of MPN142 in relation to inter-RepMP5 recombination, we determined the sequences of all RepMP5 elements in a collection of 25 strains. The results indicate that: (i) inter-RepMP5 recombination events have occurred in seven of the strains, and (ii) putative RepMP5 recombination events involving MPN142 have induced amino acid changes in a surface-exposed part of the P40 protein in two of the strains. We conclude that recombination between RepMP5 elements is a common phenomenon that may lead to sequence variation of MPN142-encoded proteins.
Mediation of CTCF transcriptional insulation by DEAD-box RNA-binding protein p68 and steroid receptor RNA activator SRA
Authors: Yao Hongjie , Brick Kevin , Evrard Yvonne , Xiao Tiaojiang , Camerini-Otero R. Daniel , Felsenfeld Gary
Published: October 2010

CCCTC-binding factor (CTCF) is a DNA-binding protein that plays important roles in chromatin organization, although the mechanism by which CTCF carries out these functions is not fully understood. Recent studies show that CTCF recruits the cohesin complex to insulator sites and that cohesin is required for insulator activity. Here we showed that the DEAD-box RNA helicase p68 (DDX5) and its associated noncoding RNA, steroid receptor RNA activator (SRA), form a complex with CTCF that is essential for insulator function. p68 was detected at CTCF sites in the IGF2/H19 imprinted control region (ICR) as well as other genomic CTCF sites. In vivo depletion of SRA or p68 reduced CTCF-mediated insulator activity at the IGF2/H19 ICR, increased levels of IGF2 expression, and increased interactions between the endodermal enhancer and IGF2 promoter. p68/SRA also interacts with members of the cohesin complex. Depletion of either p68 or SRA does not affect CTCF binding to its genomic sites, but does reduce cohesin binding. The results suggest that p68/SRA stabilizes the interaction of cohesin with CTCF by binding to both, and is required for proper insulator function.