bluuebunny/crossref_metadata_2025 huggingface dataset:
The effect of linguistic proficiency, age of second language acquisition, and length of exposure to a new cultural environment on bilinguals' divergent thinking
Authors: KHARKHURIN ANATOLIY V.
Published: June 2008

The study argues that, in addition to advantages in conscious attention-demanding processing, bilinguals may also exhibit enhanced unconscious divergent thinking. To investigate this issue, the performance of Russian–English bilingual immigrants and English monolingual native speakers was compared on the Abbreviated Torrance Test for Adults, which is a traditional assessment tool of divergent thinking. The study reveals bilinguals' superiority on divergent thinking tasks that require the ability to simultaneously activate and process multiple unrelated concepts from distant categories. Divergent thinking was facilitated by bilinguals' proficiency in two languages, the age of acquisition of these languages and the length of exposure to the new cultural settings that accompanies the acquisition of a new language. A specific architecture of bilingual memory in which two lexicons are mutually linked to the shared conceptual system is theorized to facilitate the functioning of the language mediated concept activation, thereby encouraging bilinguals' divergent thinking performance.
RECOGNIZING STRONG RANDOM REALS
Authors: OSHERSON DANIEL , WEINSTEIN SCOTT
Published: June 2008

The class of strong random reals can be defined via a natural conception of effective null set. We show that the same class is also characterized by a learning-theoretic criterion of ‘recognizability’.
ON ADOPTING KRIPKE SEMANTICS IN SET THEORY
Authors: INCURVATI LUCA
Published: June 2008

Several philosophers have argued that the logic of set theory should be intuitionistic on the grounds that the open-endedness of the set concept demands the adoption of a nonclassical semantics. This paper examines to what extent adopting such a semantics has revisionary consequences for the logic of our set-theoretic reasoning. It is shown that in the context of the axioms of standard set theory, an intuitionistic semantics sanctions a classical logic. A Kripke semantics in the context of a weaker axiomatization is then considered. It is argued that this semantics vindicates an intuitionistic logic only insofar as certain constraints are put on its interpretation. Wider morals are drawn about the restrictions that this places on the shape of arguments for an intuitionistic revision of the logic of set theory.
PROBABILISTIC CONDITIONALS ARE ALMOST MONOTONIC
Authors: JOHNSON MATTHEW P. , PARIKH ROHIT
Published: June 2008

One interpretation of the conditional If P then Q is as saying that the probability of Q given P is high. This is an interpretation suggested by Adams (1966) and pursued more recently by Edgington (1995). Of course, this probabilistic conditional is nonmonotonic, that is, if the probability of Q given P is high, and R implies P, it need not follow that the probability of Q given R is high. If we were confident of concluding Q from the fact that we knew P, and we have stronger information R, we can no longer be confident of Q. We show nonetheless that usually we would still be justified in concluding Q from R. In other words, probabilistic conditionals are mostly monotonic.
ULTIMATE TRUTHVIS-À-VISSTABLE TRUTH
Authors: WELCH P. D.
Published: June 2008

We show that the set ofultimately truesentences in Hartry Field's Revenge-immune solution model to the semantic paradoxes is recursively isomorphic to the set ofstably truesentences obtained in Hans Herzberger's revision sequence starting from the null hypothesis. We further remark that this shows that a substantial subsystem of second-order number theory is needed to establish the semantic values of sentences in Field's relative consistency proof of his theory over the ground model of the standard natural numbers:\Delta _3^1-CA0(second-order number theory with a\Delta _3^1-comprehension axiom scheme) is insufficient. We briefly consider his claim to have produced a ‘revenge-immune’ solution to the semantic paradoxes by introducing this conditional. We remark that the notion of a ‘determinately true’ operator can be introduced in other settings.
Self-Regulated Learning as a Competence
Authors: Wirth Joachim , Leutner Detlev
Published: June 2008

Lively research on self-regulated learning has produced a great number of models of self-regulated learning competence and it is still a challenge to integrate them within a single coherent framework. However, such a framework is necessary for, among other reasons, the development of valid assessment methods. We argue that one common characteristic of all models is that they consider the competence to make solid comparisons as a key competence of self-regulated learning. However, the kind of comparisons and the kind of standards used for these comparisons differ between models. The same is true for assessment methods. Valid assessment methods also have implemented comparisons and they also differ concerning the kind of comparison and the kind of standards used for assessment. In order to categorize both, models as well as assessment methods, we propose to distinguish between component models and process models of self-regulated learning. Component models imply the use of offline standards for assessment whereas process models imply the use of online standards. Both offline and online standards can be either quantitative or qualitative. We show that using qualitative standards leads to a higher validity of the assessment than using quantitative standards. This advantage of qualitative standards can be shown for both offline standards as well as online standards.
In‐flight validation of Aura MLS ozone with CAFS partial ozone columns
Authors: Petropavlovskikh I. , Froidevaux L. , Shetter R. , Hall S. , Ullmann K. , Bhartia P. K. , Kroon M. , Levelt P.
Published: June 2008

A comprehensive data set of partial ozone columns was derived from the charge‐coupled device (CCD) Actinic Flux Spectroradiometer (CAFS) measurements taken during the Polar 2005, Houston 2005, and Costa Rica 2006 Aura Validation Experiments (AVE). It was used to validate the colocated daytime Aura Microwave Limb Sounder (MLS) partial ozone columns along the aircraft tracks over diverse geophysical conditions. Results show that the MLS v.1.5 and CAFS ozone columns agree to better than 3% at pressure levels of 100 and 146 hPa, and to better than 5% at 215 hPa level. The partial ozone column differences between the two systems were the largest during the Polar AVE (PAVE) 2005 campaign (polar region, ∼250 hPa pressure level), and the smallest during the CRAVE 2006 campaign (tropics, ∼100 hPa pressure level). Overall, the averaged bias between the MLS and CAFS partial ozone column is about 2%, and the standard deviation of the differences is about 2%. The v.2.2 update of the MLS data tends to reduce the bias to less than 1%. In addition, the AVE 2005 campaign uncovered an altitude‐dependent bias, where the MLS partial ozone columns above 100 and 146 hPa pressure levels were about 1% higher than the CAFS derived columns, while the bias increased to about 3 % in partial columns integrated above 215 hPa. However, the MLS and CAFS data track each other closely over a wide range of atmospheric conditions, and the differences lie within the combined uncertainties of the two data sets.
Magnetization behavior and magnetic viscosity in nanostructured PrCo4.5C0.5 ribbons
Authors: Yang Bai , Shen Bao-Gen , Zhao Tong-Yun , Sun Ji-Rong
Published: June 2008

The magnetization processes in nanocomposite PrCo4.5C0.5 ribbons that are composed of two hard magnetic phases PrCo5Cδ and Pr5Co19Cε have been systematically investigated. The magnetic reversal of the samples is found to be mainly determined by inhomogeneous domain wall pinning. Different from the nanocomposite magnets with hard and soft magnetic phases, the reverse field, where the reversible susceptibility χrev peaks, is found to be 5.8kOe, which is much lower than the field corresponding to the χtotal maximum. The study of magnetic viscosity indicates that the time dependence of magnetization is primarily determined by the reversal of PrCo5Cδ phases, and a larger activation volume, v=3.2×10−18cm3, is deduced for the PrCo4.5C0.5 ribbons.
Size dependent acoustic phonon dynamics of CdTe0.68Se0.32 nanoparticles in borosilicate glass
Authors: Gupta Sanjeev K. , Jha Prafulla K. , Arora A. K.
Published: June 2008

Low frequency acoustic vibration and phonon linewidth for CdTe0.68Se0.32 nanoparticle embedded in borosilicate glass are calculated using two different approaches by considering the elastic continuum model and fixed boundary condition. The presence of medium significantly affects the phonon peaks and results into the broadening of the modes. The linewidth is found to depend inversely on the size, similar to that reported experimentally. The damping time and quality factor have also been calculated. The damping time that is of the order of picoseconds decreases with the decrease in size. High value of quality factor for l=2 normal mode suggests the less loss of energy for this mode.
Subcutoff microwave driven plasma ion sources for multielemental focused ion beam systems
Authors: Mathew Jose V. , Chowdhury Abhishek , Bhattacharjee Sudeep
Published: June 2008

A compact microwave driven plasma ion source for focused ion beam applications has been developed. Several gas species have been experimented including argon, krypton, and hydrogen. The plasma, confined by a minimum B multicusp magnetic field, has good radial and axial uniformity. The octupole multicusp configuration shows a superior performance in terms of plasma density (∼1.3×1011cm−3) and electron temperature (7–15eV) at a power density of 5–10W∕cm2. Ion current densities ranging from a few hundreds to over 1000mA∕cm2 have been obtained with different plasma electrode apertures. The ion source will be combined with electrostatic Einzel lenses and should be capable of producing multielemental focused ion beams for nanostructuring and implantations. The initial simulation results for the focused beams have been presented.
Structure, paramagnetic defects and light-emission of carbon-rich a-SiC:H films
Authors: Vasin A. V. , Kolesnik S. P. , Konchits A. A. , Rusavsky A. V. , Lysenko V. S. , Nazarov A. N. , Ishikawa Y. , Koshka Y.
Published: June 2008

The effect of vacuum annealing on local structure reconstruction, evolution of photoluminescence (PL) and paramagnetic defects in carbon-rich a-Si1−xCx:H films (x=0.7) was studied. Strong enhancement of visible (white-green) PL was observed after annealing in the temperature range of 400–500 °C. Such enhancement was correlated with increasing of the concentration of carbon-hydrogen bonds in Si:CHn accompanied with increase in the fluctuation of the interatomic potential. Complete disappearance of PL, “graphitization” of the carbon precipitates, and a strong increase in the concentration of the paramagnetic states were observed after annealing at 650 °C and above. The enhancement and the degradation of PL after different-temperature treatments are explained by the following competing effects: (1) enhancement of the radiative recombination due to passivation of paramagnetic defects with hydrogen and increase of localization of photoexcited electron-hole pairs due to formation of new Si:CH and (2) enhancement of the nonradiative recombination through the paramagnetic states due to increase in their concentration caused by graphitization of carbon precipitates after high- temperature treatment.
An industry applicable model for predicting lean meat yield in lamb carcasses
Authors: Hopkins D. L.
Published: June 2008

A wide selection of lamb types (n = 360) of mixed sex (ewes and wethers) were slaughtered at a commercial abattoir. Soft tissue depth at the GR site (thickness of tissue over the 12th rib, 110 mm from the midline) was measured in the chiller, using a GR knife (GR). Each carcass was subsequently broken down to a range of trimmed boneless retail cuts and the lean meat yield determined. The predominant industry model for predicting meat yield in Australia uses hot carcass weight (HCW) and tissue depth at the GR site. A moderate level of accuracy and precision was found when HCW and GR were used to predict lean meat yield (R2 = 40.5, r.s.d. = 2.39%), which could be improved markedly when loin muscle cross-sectional area at the 12th rib (EMA) was included in the model (R2 = 54.5, r.s.d. = 2.10%). A better result was achieved when the model included the weight of subcutaneous fat (SLFat) from the shortloin (R2 = 73.8, r.s.d. = 1.59%). A combination of SLFat and the weight of the shortloin muscle (SLMus) negated the need to include either GR or EMA in the model (R2 = 76.1, r.s.d. = 1.52%). The transportability of a model based on HCW, SLFat and SLMus was tested by randomly dividing the dataset and comparing the coefficients and the level of accuracy and precision. Collecting measures of EMA, SLFat and SLMus in boning rooms is potentially feasible. If this can be achieved under commercial conditions, a rigorous method for automatically predicting lean meat yield during boning could be applied. Application of the approach to large-scale research programs, where estimates of lean meat yield are required, would be possible at a reduced cost compared with alternative systems based on full carcass breakdown. A suitable model is given for this purpose.
Mild congenital goitre increases lamb mortality in southern New South Wales
Authors: Robertson S. M. , Friend M. A. , King B. J.
Published: June 2008

Congenital goitre, symptomatic of iodine deficiency, can be associated with elevated levels of lamb mortality. This study details an outbreak east of Wagga Wagga in southern NSW, where goitre has previously not been documented. Measurements were taken on flocks at two sites near Ladysmith. Up to 82% of dead lambs had thyroid : weight ratios of more than 0.4 g/kg bodyweight, potentially large enough to affect survival. Up to 16% of lambs surviving to marking had enlarged thyroids (i.e. estimated by palpation). Lambs with enlarged thyroids may be more prone to dystocia, with ewes requiring assistance at delivery. Sex and birthweight were not related to thyroid size, but of lambs surviving to marking, a greater proportion of Merino than crossbred lambs had enlarged thyroids. At the second site, growth rate from birth to marking but not to weaning was reduced in lambs with higher thyroid scores. The high incidence of goitre in these flocks suggests that iodine deficiency may be an important factor in lamb mortality in some years in this region, but is unlikely to be detected due to the relatively small degree of thyroid enlargement.
Preslaughter management practices influence carcass characteristics of young goats
Authors: Greenwood P. L. , Finn J. A. , May T. J. , Nicholls P. J.
Published: June 2008

Effects of sex, weaning 3 weeks before slaughter, continuous fasting and water deprivation for up to 72 h, and initial liveweight (LW) and body condition score (CS) on LW and carcass characteristics were studied in 231 goats of ~16 weeks of age with a LW of 13.6 ± 2.4 kg (mean ± s.d.). Overall, the animals lost 5.9% of initial LW during the first 12 h of fasting, 7.5% by 24 h, 10.8% by 48 h and 14.1% by 72 h. Weaned goats lost 2.6% more LW than non-weaned goats after 48 h fasting, and animals denied access to water lost 1.5% more LW than those with access to water. Fasting period, weaning status, water availability and CS influenced dressing out percentage determined as percentage initial LW or percentage preslaughter LW. All six factors investigated significantly influenced hot carcass weight (HCW), retail meat yield (kg) and L2 (lumbar eye muscle site) tissue depth. Sex, weaning, fasting period, and initial LW and CS influenced retail meat yield (as a percentage of HCW) and GR (12th rib) tissue depth. Muscle colour score was affected by initial LW, water availability and fasting period. There was also a fasting period × sex interaction for muscle colour. The results provide information for estimation of carcass characteristics of young goats marketed for meat and demonstrate that preslaughter management of young goats influences factors that affect economic returns. They reinforce the need to minimise time off feed and water before slaughter of young goat kids, from both a welfare and an economic perspective, and for further research on preslaughter management factors that may influence welfare of goats and goat meat quality.
Effect of loading practices and 6-hour road transport on the physiological responses of yearling cattle
Authors: Pettiford S. G. , Ferguson D. M. , Lea J. M. , Lee C. , Paull D. R. , Reed M. T. , Hinch G. N. , Fisher A. D.
Published: June 2008

A controlled study using 16 yearling Angus steers was conducted to determine the physiological responses associated with loading practices followed by 6 h of road transport and 17 h of post-transport recovery. The cattle were quietly mustered from grazing at pasture and directly loaded onto a truck for transport. During loading, cattle received either four consecutive prods with a commercial electric prodder (n = 8) or no prodding (control, n = 8). The experiment was performed in four replicates, conducted on consecutive days, with four animals (n = 2 per treatment) utilised on each day. On the truck, cattle were confined to pens that each held a single animal facing the direction of travel. Blood samples were taken via jugular catheters before and during the 6 h journey and during the 17 h recovery phase. Samples were analysed for haematology, osmolality and plasma cortisol, total protein, creatine kinase, blood urea nitrogen and the acute phase protein haptoglobin. The physiological measurements indicated that most stress occurred during loading and the initial stages of transport, but after this, the cattle habituated and were able to cope with the 6 h of transport. After 17 h of recovery, nearly all the variables measured had returned to their pre-transport levels. Use of an electric prodder during loading did not modify the physiological responses to loading, transport or the rate of recovery compared with the controls.
Preweaning feed exposure and different feed delivery systems to enhance feed acceptance of sheep
Authors: Savage D. B. , Ferguson D. M. , Fisher A. D. , Hinch G. N. , Mayer D. G. , Duflou E. , Lea J. M. , Baillie N. D. , Raue M.
Published: June 2008

Prior exposure of sheep to a novel feed has been shown to expedite the acceptance of that feed later in life. This study was designed to investigate the benefits of early social transmission of feed recognition for productivity and feeding behaviour of sheep in a feedlot. On a research farm near Armidale, Australia, 175 12-week-old Merino × Dorset lambs, together with their dams, were exposed to one of three preweaning treatments: (i) no exposure to feedlot pellets, (ii) offered feedlot pellets on the pasture, or (iii) offered feedlot pellets in feed troughs. The feedlot pellets were offered on two occasions at a rate of 200 g/dam, 1 month before weaning. After weaning, from 18 weeks of age, the lambs were observed for feeding behaviour and their growth during a 50-day feedlot finishing phase. Preweaning exposure to the pellets and the feed delivery system increased the rate of feed acceptance; however, there was no difference in the growth of lambs between the preweaning treatments at the end of the feedlot phase. The difference in percentage of lambs not eating between treatment groups was most pronounced during the first 2 days of the feeding period, with the differences gradually diminishing over the initial week of the feedlot phase. It is considered that differences in feedlot performance due to rate of acceptance of novel feeds are more likely under commercial conditions where pen densities are higher and feed ration transitions may be more rapid.
Feed efficiency for meat and wool production by Merino and F1 Dohne×Merino lambs fed pelleted diets of different nutritive value
Authors: Van Beem D. , Wellington D. , Paganoni B. L. , Vercoe P. E. , Milton J. T. B.
Published: June 2008

There is anecdotal evidence from Western Australian breeders that Dohne sheep maintain a higher level of meat and wool production than Australian Merinos. Feed efficiency, carcass and wool attributes are moderately heritable so we hypothesised there would be differences in these traits between Merino and F1 Dohne × Merino lambs. Two groups of 15 Merino and 15 F1 Dohne × Merino wether lambs (29–40 kg) were fed a pelleted diet of either moderate or high energy and protein content for 48 days. Ad libitum pellet intake and liveweight gain were measured and the feed conversion ratio (FCR) for both wool growth and liveweight were calculated. Wool growth and quality were measured and the lambs were slaughtered to measure carcass and meat quality attributes. The F1 Dohne lambs were heavier at the start of the study and grew faster than the Merinos (P < 0.05) irrespective of diet. Consequently, the carcasses of the F1 Dohne lambs were heavier than the Merinos (P < 0.001), but the differences in FCR were not significant. Merino lambs produced more clean wool of lower fibre diameter from less feed than the F1 Dohne lambs (P < 0.05). These results suggest that F1 Dohne × Merino lambs may have an economic advantage in terms of meat production, but this is traded-off against wool production.
Towards the development of generic and differentiated models of educational effectiveness: A study on school and teacher effectiveness in physical education
Authors: Kyriakides Leonidas , Tsangaridou Niki
Published: June 2008

This article presents the results of an evaluation study in Physical Education (PE) in which 23 schools, 49 classes and 1142 year 4 Cypriot students participated. This study attempted to identify the extent to which a theoretical framework of educational effectiveness research based on Creemers' model can be developed. The relationship between generic and differentiated effectiveness was also examined. Most of the variables in Creemers' model showed the expected effects, irrespective of the criterion used to measure effectiveness in PE. The great majority of teachers were found to be equally effective in achieving different aims of PE. There was some variability in the effectiveness status of most teachers who were expected to teach PE in classrooms of different schools. Implications of findings for the development of generic and differentiated models of educational effectiveness are drawn.
The use of virtual reality for training in carotid artery stenting: a construct validation study
Authors: Berry M. , Reznick R. , Lystig T. , Lönn L.
Published: June 2008

Background: Given that carotid artery stenosis (CAS) intervention is procedurally difficult, possesses an extensive learning curve, and involves a grave list of potential complications, construct validation of new non-clinical training devices is of increasing importance.

Purpose: To evaluate the construct validity of the Procedicus-Virtual Interventional Simulator Trainer (Procedicus-VIST) and its use as a training tool.

Material and Methods: Sixteen interventionalists (15 males, one female; mean interventional radiology [IR] experience >11 years) and 16 medical students (15 males, one female; no IR experience) received 1 hour of didactic instruction followed by an hour of familiarization training. Subjects then attempted to complete a carotid artery stenting procedure within 1 hour while their performance metrics were recorded. All participants completed a qualitative exit survey of subjective parameters using a visual analog scale.

Results: Procedure and fluoroscopic time was 8.7 and 8.7 min greater in the novice group ( P=0.0066 and P=0.0031), respectively. There were no significant differences in performances between the two groups in the remaining metrics of cine loops (number recorded), tool/vessel ratio, coverage percentage, and placement accuracy or residual stenosis. Contrast measurement metrics were found to be too imprecise for statistical analysis. Experienced and novice opinions differed significantly for six of 10 subjective parameters. No statistically significant difference in video-gaming habits was demonstrated.

Conclusion: With the exception of the metrics of performance time and fluoroscopic use, construct validity of the Procedicus-VIST carotid metrics were not confirmed. Virtual reality simulation as a training method was valued more by novices than by experienced interventionalists.
Underdiagnosis of vertebral collapse on routine multidetector computed tomography scan of the abdomen
Authors: Obaid H. , Husamaldin Z. , Bhatt R.
Published: June 2008

Background: Vertebral fractures are commonly associated with osteoporosis and have significant morbidity and mortality rates. Osteoporotic vertebral fractures are presently considered as a treatable and preventable condition, and early detection is vital for further management. The evaluation of vertebral compression on multidetector computed tomography (MDCT) scans of the abdomen has, to our knowledge, not been reported before.

Purpose: To assess the prevalence of vertebral collapse on routine abdominal CT scans, and to evaluate the usefulness of the multiplanar reconstruction (MPR) capability of MDCT scans in accurately identifying vertebral abnormalities such as vertebral collapse, spondylolisthesis, and retrolisthesis.

Material and Methods: A retrospective review of 307 MDCT scans of the abdomen was carried out at a university teaching hospital. Identifiable patient information was anonymized for data protection. All images were reviewed on a picture archiving and communications system (PACS) using sagittal MPR and bone window for the assessment of the vertebrae. Data were collected from the Computerized Radiology Information System (CRIS).

Results: Vertebral collapse was seen in 42 (13.6%) of the 307 patients undergoing routine MDCT of the abdomen. Multilevel and single-level collapses were seen in 24 and 18 patients, respectively. Spondylolisthesis was identified in 5.5% ( n=17), and retrolisthesis was seen in 0.6% ( n=2). All patients with vertebral fracture were older than 50 years. Women were more commonly affected than men.

Conclusion: A significant number of patients with vertebral collapse were diagnosed using MPR on MDCT routine scans of the abdomen.
Prevalence of coronary artery intramyocardial course in a large population of clinical patients detected by multislice computed tomography coronary angiography
Authors: De Rosa R. , Sacco M. , Tedeschi C. , Pepe R. , Capogrosso P. , Montemarano E. , Rotondo A. , Runza G. , Midiri M. , Cademartiri F.
Published: June 2008

Background: Intramyocardial course, an inborn coronary anomaly, is defined as a segment of a major epicardial coronary artery that runs intramurally through the myocardium; in particular, we distinguish myocardial bridging, in which the vessel returns to an epicardial position after the muscle bridge, and intramyocardial course, which is described as a vessel running and ending in the myocardium.

Purpose: To evaluate the prevalence of myocardial bridging and intramyocardial course of coronary arteries as defined by multidetector computed tomography (MDCT) angiography.

Material and Methods: The study population consisted of 242 consecutive patients (211 men, 31 women; mean age 59±6 years) with atypical chest pain admitted to our hospital between December 2004 and September 2006. All MDCT examinations were performed using a 16-detector-row scanner (Aquilion 16 CFX; Toshiba Medical System, Tokyo, Japan). Patients with heart rate above 65 bpm received 50 mg atenolol orally for 3 days prior to the MDCT scan, or they increased their usual therapy with beta-blockers, in order to obtain a prescan heart rate <60 bpm. Curved multiplanar and 3D volume reconstructions were performed to explore coronary anatomy.

Results: In 235 patients, the CT scan was successful and images were appropriate for evaluation. The prevalence of myocardial bridging and intramyocardial course of coronary arteries was 18.7% (47 cases) in our patient population. In 30 segments (63.8%), the vessels ran and ended in the myocardium. In the remaining 17 segments (36.2%), the vessels returned to an epicardial position after the muscle bridge. We found no difference in the prevalence of this inborn coronary anomaly when comparing different clinical characteristics of the study population (sex, age, body-mass index [BMI], etc.). The mean length of the subepicardial artery was 7 mm (range 5–12 mm), and the mean depth in the diastolic phase was 1.9 mm (range 1.2–2.3 mm). There was no significant difference of diameter in these segments between the different R–R phases examined.

Conclusion: Our study is in agreement with major angiographic literature reporting a prevalence of myocardial bridging and intramyocardial course between 0.5% and 33%. MDCT technology represents a useful, noninvasive imaging method to assess and evaluate the location, depth, and length of this anatomical variation.
Processing Polarity: How the Ungrammatical Intrudes on the Grammatical
Authors: Vasishth Shravan , Brüssow Sven , Lewis Richard L. , Drenhaus Heiner
Published: June 2008

A central question in online human sentence comprehension is, “How are linguistic relations established between different parts of a sentence?” Previous work has shown that this dependency resolution process can be computationally expensive, but the underlying reasons for this are still unclear. This article argues that dependency resolution is mediated by cue‐based retrieval, constrained by independently motivated working memory principles defined in a cognitive architecture. To demonstrate this, this article investigates an unusual instance of dependency resolution, the processing of negative and positive polarity items, and confirms a surprising prediction of the cue‐based retrieval model: Partial‐cue matches—which constitute a kind of similarity‐based interference—can give rise to the intrusion of ungrammatical retrieval candidates, leading to both processing slow‐downs and even errors of judgment that take the form of illusions of grammaticality in patently ungrammatical structures. A notable achievement is that good quantitative fits are achieved without adjusting the key model parameters.
Microcystin concentrations and cell quotas in Saginaw Bay, Lake Huron
Authors: Fahnenstiel G. L. , Millie D. F. , Dyble J. , Litaker R. W. , Tester P. A. , McCormick M. J. , Rediske R. , Klarer D.
Published: June 2008

Distribution of the toxin microcystin was studied in Saginaw Bay, Lake Huron during two summer (August) cruises in 2003–2004. Intracellular microcystin concentrations averaged 1.1 μ g l− 1 (range 0.01–3.5 μ g l− 1), and extracellular concentrations averaged only 0.09 μ g l− 1 (range 0.01–0.18 μ g l− 1). Highest microcystin concentrations were found in the nearshore regions of the bay, which were shallow and had high total phosphorus concentrations. Microcystin concentrations were strongly correlated with Microcystis aeruginosa abundance (r = 0.8). M. aeruginosa abundance was strongly correlated with total phosphorus, and growth rates were negatively correlated with C:P ratio. Particulate nutrient ratios suggested that Saginaw Bay algae were severely phosphorus deficient. Microcystin cell quotas for M. aeruginosa averaged 140 fg cell− 1, and were not correlated with any environmental factor or growth rates. In Saginaw Bay, phosphorus availability primarily influences microcystin concentrations through direct control of M. aeruginosa abundance and growth rates, and not through direct control of cellular microcystin synthesis.
Systematic biological prioritization after a genome-wide association study: an application to nicotine dependence
Authors: Saccone Scott F. , Saccone Nancy L. , Swan Gary E. , Madden Pamela A. F. , Goate Alison M. , Rice John P. , Bierut Laura J.
Published: June 2008

Motivation: A challenging problem after a genome-wide association study (GWAS) is to balance the statistical evidence of genotype–phenotype correlation with a priori evidence of biological relevance.

Results: We introduce a method for systematically prioritizing single nucleotide polymorphisms (SNPs) for further study after a GWAS. The method combines evidence across multiple domains including statistical evidence of genotype–phenotype correlation, known pathways in the pathologic development of disease, SNP/gene functional properties, comparative genomics, prior evidence of genetic linkage, and linkage disequilibrium. We apply this method to a GWAS of nicotine dependence, and use simulated data to test it on several commercial SNP microarrays.

Availability: A comprehensive database of biological prioritization scores for all known SNPs is available at http://zork.wustl.edu/gin. This can be used to prioritize nicotine dependence association studies through a straightforward mathematical formula—no special software is necessary.

Contact:  ssaccone@wustl.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Public Status and Prevalence of Acupuncture in Japan
Authors: Ishizaki Naoto , Yano Tadashi , Kawakita Kenji
Published: June 2008

Acupuncture originated in China and is widespread throughout Asia. It is expected that a higher utilization of this remedy exists in these countries compared to Western countries. We conducted annual nationwide surveys from 2003 through 2006 on the utilization of acupuncture in Japan. Face‐to‐face interviews were conducted with 2000 individuals randomly chosen from the resident database. Annual utilization percentages, based on the number of respondents, from 2003 to 2006 were 6.5%, 4.8%, 6.4%, and 6.7%, respectively, while lifetime experiences determined in each surveys were estimated as 26.7, 19.4, 24.4 and 25.4, respectively. Respondents who had utilized acupuncture and/or moxibustion tended to be older than those who had no experience. Acupuncture was mainly used for musculoskeletal symptoms, and a detailed breakdown of the musculoskeletal symptoms identified in the 2005 survey showed 50.9% for low back pain, 35.9% for shoulder stiffness and 12.0% for knee pain. Reasons given for continuing therapy included the effective amelioration of symptoms, comfort of the procedure and low number of side‐effects, while those who decided against continuing cited no improvement of symptoms, cost and lack of time for treatment. In conclusion, annual utilization of acupuncture and/or moxibustion was estimated at more than 6%, and the percentage of those with a lifetime experience was ∼25%, thus demonstrating the relatively higher utilization of the remedy in Japan over utilization in western countries. Application of the treatment for musculoskeletal problems and utilization by the older population were specific standouts of the use of acupuncture and/or moxibustion in Japan.
Megafauna community structure and trophic relationships at the recently discovered Concepción Methane Seep Area, Chile, ∼36°S
Authors: Sellanes J. , Quiroga E. , Neira C.
Published: June 2008

Sellanes, J., Quiroga, E., and Neira, C. 2008. Megafauna community structure and trophic relationships at the recently discovered Concepción Methane Seep Area, Chile, ∼36°S. – ICES Journal of Marine Science, 65: 1102–1111. The fauna, community composition, and trophic support of the newly discovered Concepción Methane Seep Area (CMSA) are compared with those at a nearby non-seep control. The assemblage of chemosymbiotic bivalves is defined by eight species, including the families Lucinidae, Thyasiridae, Solemyidae, and Vesicomyidae. Seep polychaetes are represented by Lamellibrachia sp. and two commensal species of the vesicomyid Calyptogena gallardoi. Although taxonomic analysis is still under way, most of the chemosymbiotic species seem to be endemics. The CMSA is a hotspot for non-seep benthic megafauna too; 101 taxa were present, but most of them are colonists or vagrants (i.e. not endemics of methane seeps). Isotope analysis supported the belief that non-symbiont-bearing species utilize photosynthetically fixed carbon, because they were isotopically distinct from the chemosymbiotic bivalve species present. It is our opinion that, at this site, which underlies one of the most productive coastal upwelling regions of the world, spatial heterogeneity and the availability of hard substratum, generated by the presence of authigenic carbonate crusts, are more important factors in attracting non-seep fauna than the availability of locally produced chemosynthetic food.
Enzyme Susceptibility of High‐Amylose Starch Precipitated from Sodium Hydroxide Dispersions
Authors: Evans Annette , Thompson Donald B.
Published: June 2008

Type III resistant starch (RS) is understood to be due to the ordered structure formation in the process of retrogradation. Most treatments of granular high‐amylose maize starch (HAMS) do not completely eliminate the original ordered structure. We hypothesized that residual ordered structure would constrain subsequent physical reassociation of chains and the formation of RS. The objective was to generate differences in enzyme susceptibility using two means of precipitation of fully dispersed starch and to relate differences in enzyme susceptibility to the structure of the precipitates. Dispersions in sodium hydroxide were precipitated either with ethanol or ammonium sulfate. RS and the timecourse of digestion were determined. Crystallinity and helicity were estimated using wide‐angle X‐ray diffraction and solid‐state 13C CP/MAS NMR, respectively. Precipitation of whole starch with ethanol led to lower RS values (≈24%) than precipitation with ammonium sulfate (≈39%) and also to higher reaction rate constants for an early component of digestion. Ethanol precipitation of a branched starch fraction gave essentially no RS, whereas ammonium sulfate precipitation of the same branched material had >20% RS. Ethanol precipitates contained single helices, in most but not all cases, contributing to V‐type crystallinity. Ammonium sulfate precipitates had double helices contributing to B‐type crystallinity.
Chaste: using agile programming techniques to develop computational biology software
Authors: Pitt-Francis Joe , Bernabeu Miguel O , Cooper Jonathan , Garny Alan , Momtahan Lee , Osborne James , Pathmanathan Pras , Rodriguez Blanca , Whiteley Jonathan P , Gavaghan David J
Published: June 2008

Cardiac modelling is the area of physiome modelling where the available simulation software is perhaps most mature, and it therefore provides an excellent starting point for considering the software requirements for the wider physiome community. In this paper, we will begin by introducing some of the most advanced existing software packages for simulating cardiac electrical activity. We consider the software development methods used in producing codes of this type, and discuss their use of numerical algorithms, relative computational efficiency, usability, robustness and extensibility.

We then go on to describe a class of software development methodologies known as test-driven agile methods and argue that such methods are more suitable for scientific software development than the traditional academic approaches. A case study is a project of our own, Cancer, Heart and Soft Tissue Environment, which is a library of computational biology software that began as an experiment in the use of agile programming methods. We present our experiences with a review of our progress thus far, focusing on the advantages and disadvantages of this new approach compared with the development methods used in some existing packages.

We conclude by considering whether the likely wider needs of the cardiac modelling community are currently being met and suggest that, in order to respond effectively to changing requirements, it is essential that these codes should be more malleable. Such codes will allow for reliable extensions to include both detailed mathematical models—of the heart and other organs—and more efficient numerical techniques that are currently being developed by many research groups worldwide.
The concentration of oxazepam and oxazepam glucuronide in oral fluid, blood and serum after controlled administration of 15 and 30 mg oxazepam
Authors: Smink Beitske E. , Hofman Berendina J. A. , Dijkhuizen Albert , Lusthof Klaas J. , De Gier Johan J. , Egberts Antoine C. G. , Uges Donald R. A.
Published: June 2008

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• Concentration–time profiles of drugs in oral fluid generally run parallel to those in blood.

• In general, oral fluid contains more parent drug than metabolites.

• For some benzodiazepines it has been shown that concentrations are lower in oral fluid than in blood.

WHAT THIS STUDY ADDS

• The concentration–time profile of oxazepam in oral fluid after a single dose of oxazepam runs parallel to blood and is dose dependent.

• Concentration ratios (oral fluid/blood and oral fluid/serum) of oxazepam and oxazepam glucuronide after controlled intake of a single dose of oxazepam are presented.

AIMS

To measure and compare the concentration–time profiles of oxazepam and oxazepam glucuronide in blood, serum and oral fluid within the scope of roadside testing.

METHODS

Biological samples were collected from eight male subjects after ingestion of 15 or 30 mg oxazepam on separate dosing occasions with an interval of 7 days. The concentration–time profiles of oxazepam and oxazepam glucuronide were fitted by using a one‐compartment model.

RESULTS

For oxazepam and oxazepam glucuronide, the mean oral fluid/blood ratios were 0.05 (range 0.04–0.07) and 0.004 (range 0.002–0.006), respectively. The concentration–time profiles in oral fluid paralleled those in blood.

CONCLUSION

After oral administration of therapeutic doses of oxazepam, concentrations in oral fluid are very much lower than those in blood, and those of oxazepam glucuronide are much lower than those of the parent compound. Nevertheless, assay of oral fluid for oxazepam can be used to detect recent ingestion of the drug in drivers suspected of impaired driving performance.
Wide variation in thrombin generation in patients with atrial fibrillation and therapeutic International Normalized Ratio is not due to inflammation
Authors: Gatt A. , Van Veen J. J. , Bowyer A. , Woolley A. M. , Cooper P. , Kitchen S. , Makris M.
Published: June 2008

Atrial fibrillation (AF) is a common cardiac arrhythmia with a 5–20% annual risk of stroke. Warfarin reduces this risk by at least 60%. Despite adequate anticoagulation within the target International Normalized Ratio (INR) range of 2·0–3·0, some patients still experience thrombotic and bleeding events. It is now possible to assess the intensity of anticoagulation with automated thrombin generation (TG) tests, such as the calibrated automated thrombogram (CAT). These tests were compared and an inverse relationship was found between the INR and CAT in 143 elderly AF patients. There was equally good correlation between the concentration of factors II, VII, IX and X and the INR and TG parameters. The peak thrombin was most strongly associated with the concentration of prothrombin fragment 1 + 2 in plasma. There was wide variability in TG parameters in patients with identical INR values, sometimes up to a fourfold difference. This TG variability in individuals with the same INR is not due to inflammation, at least when the latter is measured as the concentration of factor VIII coagulant activity, von Willebrand factor antigen, high sensitivity C‐reactive protein and fibrinogen. It was concluded that, although the TG and INR were closely correlated there was wide variability in peak thrombin and endogenous thrombin potential in patients within the INR therapeutic range, the cause of which remains unclear.
A previously unidentified σ factor and two accessory proteins regulate oxalate decarboxylase expression in Bacillus subtilis
Authors: MacLellan Shawn R. , Wecke Tina , Helmann John D.
Published: June 2008

We have investigated the function of a cell envelope stress‐inducible gene, yvrI, which encodes a 22.5 kDa protein that includes a predicted σ70 region 4 domain, but lacks an apparent region 2 domain. YvrI interacts with RNA polymerase and overexpression of YvrI results in induction of OxdC, an oxalate decarboxylase maximally expressed under low‐pH conditions. We have used microarray‐based analyses to define the YvrI regulon. YvrI is required for the transcription of three operons (oxdC‐yvrL, yvrJ and yvrI‐yvrHa) each of which is preceded by a highly similar promoter sequence. Activation of these promoters requires both YvrI and the product of the second gene in the yvrI‐yvrHa operon, YvrHa. YvrI and YvrHa together allow recognition of the oxdC promoter, stimulate DNA melting and activate transcription by core RNA polymerase. Together, these results suggest that YvrI is a previously unrecognized σ factor in Bacillus subtilis and that the 9.5 kDa YvrHa protein acts as a required co‐activator of transcription. A yvrL deletion results in the upregulation of YvrI activity suggesting that YvrL is a negative regulator of YvrI‐dependent transcription, possibly functioning as an anti‐σ factor.
Holin of bacteriophage lambda: structural insights into a membrane lesion
Authors: Krupovič Mart , Bamford Dennis H.
Published: June 2008

The length of the infection cycle of double‐stranded DNA bacteriophages is controlled by phage‐encoded small integral membrane proteins, holins. Holins are the gatekeepers of the lysis process, possessing an intriguing ability to be triggered, at a precise time point, to form large holes in the cytoplasmic membrane of phage‐infected bacteria. The paper by Savva et al. in this issue of Molecular Microbiology invites us to take a closer look at this membrane lesion. For the first time, a structural characterization of large‐diameter rings formed by these peculiar membrane proteins is presented.
The FtsEX ABC transporter directs cellular differentiation in Bacillus subtilis
Authors: Garti‐Levi Sharon , Hazan Ronen , Kain James , Fujita Masaya , Ben‐Yehuda Sigal
Published: June 2008

A fundamental challenge in developmental biology is to elucidate the regulatory events that trigger cellular differentiation. Sporulation in the Gram‐positive bacterium Bacillus subtilis serves as a simple experimental model system to address this challenge. The hallmark of sporulation is the formation of an asymmetrically positioned septum that divides the cell into unequally sized progeny. Here we describe the role of an ABC transporter, comprising the FtsE and FtsX proteins, in the initiation of spore formation. We discovered that in the absence of this transporter, entry into sporulation is delayed and an atypical symmetric septum is formed instead of a polar one. We show that this phenotype can be suppressed by artificially activating the master regulator of sporulation, Spo0A, or by activating the histidine kinases that function upstream of Spo0A. Our data indicate that the FtsEX transporter is one of the top components in the hierarchy of factors required to initiate sporulation, and thus it is essential for establishing proper temporal activation of the process.