bluuebunny/crossref_metadata_2025 huggingface dataset:
Factorial Equations for Tests of Attention
Authors: Wittenborn John Richard
Published: January 2006

Tests designed to measure what was conceived to be attention were found by factor analysis to involve a factor which is independent of the factors of rote memory, visual-space, number, or perception. To a large extent, at least, this attention factor is independent of content and of mode of presentation of test material. The tests in which the variance is mainly dependent upon this factor are those involving a high degree of sustained or relatively continuous mental effort.
The Discriminant Function and its use in Psychology
Authors: Garrett Henry E.
Published: January 2006

R. A. Fisher's method of determining a set of weights for the linear combination of the scores in a battery of tests is explained and illustrated. The relationship of this method to combination by multiple regression methods is shown.
Companion Nomographs for Testing the Significance of the difference between Uncorrelated Percentages
Authors: Appel Valentine
Published: January 2006

The purpose of this article is to present a set of nomographs for testing the significance of the difference between uncorrelated percentages, and for determining necessary sample sizes when planning studies which will involve the comparison of percentages. Examples of these two uses are given as well as a description of the formula upon which the nomographs are based.
A Factorial Study of the Reasoning and Closure Factors
Authors: Botzum William A.
Published: January 2006

A battery of 46 tests was given to 237 college men. A factor analysis using the Thurstone technique revealed eight clearly interpretable first-order factors, one dubious factor, and a residual factor. The factors were interpreted as induction, deduction, flexibility of closure, speed of closure, space, verbal comprehension, word fluency, and number. Four second-order factors were abstracted from the matrix of first-order correlations. The presence of induction, deduction, and flexibility of closure on the first second-order factor, interpreted as an analytic factor, confirmed previous indications of relationships between the reasoning and closure factors. A second bipolar factor is interpreted as a speed of association factor. The third factor is interpreted as facility in handling meaningful verbal materials—perhaps an ability to do abstract thinking. The fourth factor is possibly a second-order closure factor—perhaps an ability to do concrete thinking.
Serial Correlation
Authors: Jaspen Nathan
Published: January 2006

Formulas are presented for triserial correlation, quadriserial correlation, etc., and for serial correlation in general. These formulas are based on well-known procedures outlined by Kelley, Peters and Van Voorhis, and others, and involve Pearson's correction for “broad categories.” The formula for biserial correlation also may be developed following these procedures. The assumptions underlying serial correlation are that the segmented variable is basically continuous and normally distributed, and that all the segments which together would form a whole normal distribution are present.
On Estimation of Parameters in Latent Structure Analysis
Authors: Anderson T. W.
Published: January 2006

The latent structure model considered here postulates that a population of individuals can be divided into m classes such that each class is “homogeneous” in the sense that for the individuals in the class the responses to N dichotomous items or questions are statistically independent. A method is given for deducing the proportions of the population in each latent class and the probabilities of positive responses to each item for individuals in each class from knowledge of the probabilities of positive responses for individuals from the population as a whole. For estimation of the latent parameters on the basis of a sample, it is proposed that the same method of analysis be applied to the observed data. The method has the advantages of avoiding implicitly defined and unobservable quantities, and of using relatively simple computational procedures of conventional matrix algebra, but it has the disadvantages of using only a part of the available information and of using that part asymmetrically.
A Revised Orthogonal Rotational Solution for Thurstone's Original Primary Mental Abilities Test Battery
Authors: Zimmerman Wayne S.
Published: January 2006

By extension of the rotational process, meaningful orthogonally related positions were found for all of the thirteen centroid factors which Thurstone extracted from his original PMA intercorrelations. Most of the original primary ability factors were more sharply delineated and corresponded more closely to the Army Air Force factors that bear similar names (demonstrating greater invariance from analysis to analysis). While such different results obtained by two investigators applying the same methods on the same data may initiate some concern, the results strengthen rather than weaken the idea that more psychological meaningfulness and greater invariance will result if centroid axes are rotated, using the concepts of a simple structure and positive manifold.
A Revised Law of Comparative Judgment
Authors: Harris William P.
Published: January 2006

In contrast to Thurstone's Law of Comparative Judgment, a model in which a comparison pair and its complement are assumed to give rise to two different distributions of differences is considered. The consequences of this revised model on scaling problems is developed.
An Efficient Punched-Card Method of Computing

Σ

X, ΣX2, ΣXY, and Higher Moments
Authors: Ellis Max E. , Riopelle Arthur J.
Published: January 2006

A method of computing ΣX, ΣX2, ΣXY and higher moments on IBM equipment is described. The basic method is that of successively summary punching, collating a variable number of blank cards behind these summary cards, gang-punching the data from the summary cards into the blank cards, and totalling the entries on these summary cards. The method appears to have several advantages over those previously described, especially if coded data are used.
Optimal Test Length for Maximum Absolute Prediction
Authors: Horst Paul , MacEwan Charlotte
Published: January 2006

The concepts of multiple differential prediction and multiple absolute prediction are developed in earlier papers (2, 3). The problem of determining the optimal distribution of testing time for multiple differential prediction has been previously considered (4). This paper develops an analogous procedure for multiple absolute prediction. A numerical example illustrating the procedure is presented. The mathematical rationale underlying the procedure is given.
A Significance Test for the Hypothesis that Two Variables Measure the Same Trait Except for Errors of Measurement
Authors: Lord Frederic M.
Published: January 2006

The likelihood-ratio significance test is derived for the hypothesis that after correction for attenuation two variables have a perfect correlation in the population from which the sample is drawn.
“Best Possible” Systematic Estimates of Communalities
Authors: Guttman Louis
Published: January 2006

At least four approaches have been used to estimate communalities that will leave an observed correlation matrix R Gramian and with minimum rank. It has long been known that the square of the observed multiple-correlation coefficient is a lower bound to any communality of a variable of R. This lower bound actually provides a “best possible” estimate in several senses. Furthermore, under certain conditions basic to the Spearman-Thurstone common-factor theory, the bound must equal the communality in the limit as the number of observed variables increases. Otherwise, this type of theory cannot hold for R.
A New Iterative Method for Correcting Erroneous Communality Estimates in Factor Analysis
Authors: Wherry Robert J.
Published: January 2006

A new method for correcting erroneous communality estimates is applicable to any completed orthogonal factor solution. It seeks, by direct correction of factor loadings, to make the residuals conform to the chance error criteria of zero mean and zero skewness for each row separately. Two numerical examples, with one and two factors, respectively, are presented. The method can be used as a short cut for Dwyer's extension in adding variables to a matrix. It can also be used as a short cut in cross-validation factor studies. Successful use on problems with many variables and numerous factors is claimed. Factors can be made oblique, after correction, if desired.
An Empirical Comparison of Restricted and General Latent Distance Analysis
Authors: Hays David G. , Borgatta Edgar F.
Published: January 2006

Latent distance analysis provides a probability model for the non-perfect Guttman scale; the restricted latent distance structure is simpler to compute than the general structure. Since no sampling theory for latent structure analysis is available, the advantages of the general structure cannot be expressed formally. The two structures are compared in terms of their fit to fifteen sets of empirical data. The computation schemes used are summarized.
Diagrams for Computing Tetrachoric Correlation Coefficients from Percentage Differences
Authors: Hayes Samuel P.
Published: January 2006

A description is given of diagrams (available separately) for computing tetrachoric correlation coefficients. The diagrams are entered with “per cent of combined groups above dividing point” and difference between groups in their per cents above the dividing point.
The Reliability of Component Scores
Authors: Davis Frederick B.
Published: January 2006

A method is given for determining the reliability of each of the components resulting from a factor analysis by the principal axis method.
Simulation testing of automata
Authors: Stannett Mike
Published: January 2006

Although many transducer testing techniques can establish whether a system
Imp
correctly implements a specification
Spec
, the notion of 'correctness' used in this context is often rather weak, in that it fails to distinguish correctly between behaviours that are related functionally, but distinct as processes. By appealing to the process-theoretic notion of (strong) simulation, we develop a theory of transducer, process and FSM testing capable of establishing whether
Imp
is a full simulation of
Spec
. We show, moreover, that our approach is consistent with top–down integration-testing approaches.
Phenotypic heterogeneity in biochemical parameters correlates with mutations in AGPAT2 or Seipin genes among Berardinelli–Seip congenital lipodystrophy patients
Authors: Gomes K. B. , Pardini V. Cavalcanti , Ferreira A. Clayton de Souza , Fernandes A. P.
Published: January 2006

The Berardinelli–Seip congenital lipodystrophy (BSCL) syndrome is characterized by a near‐total congenital absence of fat and predisposition to develop diabetes mellitus. We have previously reported that 22 patients from 16 consanguineous pedigrees living in the northeastern region of Brazil had a homozygous 669insA mutation in the Seipin gene (BSCL2 locus), while all of the 10 investigated subjects from the southeastern region were homozygous for a 1036 bp deletion in the AGPAT2 gene (BSCL1 locus). In this study, we compared the serum insulin and insulin resistance (HOMA), leptin, triglyceride and fasting glucose levels in individuals of these two genetically distinct clusters of BSCL subjects. The onset of diabetes was also estimated. The fasting glucose and triglyceride levels were not significantly different in these groups. Significant differences were detected for leptin, insulin and insulin resistance. BSCL1 patients presented lower serum leptin levels compared to BSCL2 patients. BSCL2 subjects had earlier onset of diabetes and higher insulin levels. In agreement, BSCL2 patients were more insulin resistant, as detected by HOMA. These results indicate phenotypic heterogeneity between BSCL1 and BSCL2 Brazilian subjects.
State regulation and response inhibition in children with ADHD and children with early‐ and continuously treated phenylketonuria: An event‐related potential comparison
Authors: Wiersema J. R. , van der Meere J. J. , Roeyers H.
Published: January 2006

Background: The presentation rate of stimuli plays an important role in explaining the performance inefficiency in children with ADHD. In general, children with ADHD have been found to perform more poorly in conditions of relatively slow event rates as compared with fast and moderate event rates. The state regulation hypothesis states that these children have problems in correcting their energetic state necessary to counteract a performance decrement, which requires extra effort allocation. In this study, we investigated state regulation in children with ADHD and used children with early‐ and continuously treated phenylketonuria (PKU) as a clinical contrast group. Method: We measured the parietal P3 during a Go/No‐Go task that incorporated a condition with a fast and a slow presentation rate. Results: We were able to show that children with ADHD, relative to controls, responded more slowly and more variably in the slow condition only, which was accompanied by a smaller P3, suggesting less effort allocation. In contrast, the children with PKU did not show a state regulation deficit. The PKU group showed prolonged stimulus evaluation processing, as indexed by P3 latency, compared to controls and children with ADHD. In addition, they made more errors of commission than the controls and the ADHD group. Conclusions: Our electrophysiological data support the state regulation hypothesis of ADHD. Only the children with PKU had more problems in inhibiting pre‐potent responding than controls, which is in accord with the prefrontal dysfunction hypothesis of PKU.
Deletion of the Caenorhabditis elegans homologues of the CLN3 gene, involved in human juvenile neuronal ceroid lipofuscinosis, causes a mild progeric phenotype
Authors: de Voer G. , van der Bent P. , Rodrigues A. J. G. , van Ommen G.‐J. B. , Peters D. J. M. , Taschner P. E. M.
Published: January 2006

The CLN3 gene is involved in juvenile neuronal ceroid lipofuscinosis (JNCL), or Batten–Spielmeyer–Vogt disease, a severe hereditary neurodegenerative lysosomal storage disorder characterized by progressive disease pathology, with loss of vision as the first symptom. Another characteristic of JNCL is the lysosomal accumulation of autofluorescent lipopigments, forming fingerprint storage patterns visible by electron microscopy. The function of the CLN3 protein is still unknown, although the evolutionarily conserved CLN3 protein is being functionally analysed using different experimental models. We have explored the potential of the nematode Caenorhabditis elegans as a model for Batten disease in order to bridge the gap between the unicellular yeast and very complex mouse JNCL models. C. elegans has three genes homologous to CLN3, for each of which deletion mutants were isolated. Cln‐3.1 deletion mutants have a decreased lifespan, and cln‐3.2 deletion mutants a decreased brood size. However, the neuronal or movement defects and aberrant lipopigment distribution or accumulation observed in JNCL were not found in the worms. To detect possible redundancy, single deletion mutants were crossed to obtain double and triple mutants, which were viable but showed no JNCL‐specific defects. The cln‐3 triple mutants show a more prominent decrease in lifespan and brood size, the latter most conspicuously at the end of the egg‐laying period, suggesting premature ageing. To focus our functional analysis we examined the C. elegans cln‐3 expression patterns, using promoter–GFP (green fluorescent protein) gene fusions. Fluorescence patterns suggest cln‐3.1 expression in the intestine, cln‐3.2 expression in the hypoderm, and cln‐3.3 expression in intestinal muscle, male‐specific posterior muscle and hypoderm. Further life stage‐ and tissue‐specific analysis of the processes causing the phenotype of the cln‐3 triple mutants may provide more information about the function of the cln‐3 protein and contribute to a better understanding of the basic processes affected in Batten disease patients.
Elevation of plasma aspartylglucosaminidase is a useful marker for the congenital disorders of glycosylation type I (CDG I)
Authors: Jackson M. , Clayton P. , Grunewald S. , Keir G. , Mills K. , Mills P. , Winchester B. , Worthington V. , Young E.
Published: January 2006

Elevated plasma aspartylglucosaminidase activity was found in 21/25 cases of CDG Ia, in single cases of CDG Ib, Ic and If, and in 15/16 cases of CDG Ix. The CDG I patients in whom the activity was not raised were either atypical clinically (CDG Ia) or very young (CDG Ih).
Methylcrotonyl‐CoA carboxylase (MCC) deficiency associated with severe muscle pain and physical disability in an adult
Authors: Boneh A. , Baumgartner M. , Hayman M. , Peters H.
Published: January 2006

We present a patient with methylcrotonyl‐CoA carboxylase (MCC) deficiency (McKusick 210200) who suffered from severe muscle pain and physical disability, and propose that this disorder be considered in the differential diagnosis of adult patients presenting with muscle pain and weakness.
Smith–Lemli–Opitz syndrome with a classical phenotype, oesophageal achalasia and borderline plasma sterol concentrations
Authors: Haas D. , Armbrust S. , Haas J.‐P. , Zschocke J. , Mühlmann K. , Fusch C. , Neumann L. M.
Published: January 2006

The diagnostic biochemical hallmarks of Smith–Lemli–Opitz syndrome (SLOS) are elevated concentrations of the cholesterol precursors 7‐ and 8dehydrocholesterol (7‐ and 8‐DHC). We describe a patient with classical SLOS phenotype and oesophageal achalasia, which has not been reported in SLOS patients before. Plasma 7‐DHC and 8‐DHC were only marginally elevated. The diagnosis was confirmed by sterol analysis in cultured skin fibroblasts and mutation analysis.
Rhabdomyolysis in early‐onset very long‐chain acyl‐CoA dehydrogenase deficiency despite normal glucose after fasting
Authors: Engbers H. M. , Dorland L. , De Sain M. G. M. , Eskes P. F. , Visser G.
Published: January 2006

A patient with very long‐chain acyl‐CoA dehydrogenase (VLCAD) deficiency presented in the neonatal period with hypoketotic hypoglycaemia and at the age of 1 year with rhabdomyolysis and normal glucose after fasting. Rhabdomyolysis may occur in the absence of hypoglycaemia in young infants as well as in older patients.
Analysis of polyols in urine by liquid chromatography–tandem mass spectrometry: A useful tool for recognition of inborn errors affecting polyol metabolism
Authors: Wamelink M. M. C. , Smith D. E. C. , Jakobs C. , Verhoeven N. M.
Published: January 2006

Several inborn errors of metabolism with abnormal polyol concentrations in body fluids are known to date. Most of these defects can be diagnosed by the assessment of urinary concentrations of polyols. We present two methods using tandem mass spectrometry for screening for inborn errors affecting polyol metabolism. Urine samples supplemented with internal standards ([13C4]erythritol, [13C2]arabitol and [2H3]sorbitol) were desalted by a mixed‐bed ion‐exchange resin. Separation was achieved by two different columns. Sugar isomers could not be separated using a Prevail Carbohydrate ES 54 column (method 1), whereas with the other column (Aminex HPX‐87C) separation of the isomers was achieved (method 2). Multiple reaction monitoring polyol detection was achieved by tandem mass spectrometry with an electron ion‐spray source operating in the negative mode. Age‐related reference ranges of polyols (erythritol, treitol, arabitol, ribitol, xylitol, galactitol, mannitol, sorbitol, sedoheptitol and perseitol) in urine were established. The applicability of the method was demonstrated by the abnormal polyol concentrations observed in patients with transaldolase deficiency, ribose‐5‐phosphate isomerase deficiency and classical galactosaemia. This paper describes two methods for the analysis of urinary polyols by liquid chromatography–tandem mass spectrometry. Method 1 is a fast screening method with the quantification of total isomers and method 2 is a more selective method with the separate quantification of the polyols. Both methods can be used for diagnosing inborn errors of metabolism affecting polyol metabolism.
Methylmalonic aciduria: Follow‐up and enzymology on the original case after 36 years
Authors: Bain M. D. , Till J. , Jones M. G. , Besley G. T. N. , Lee P. , Oliveira D. , Chalmers R. A.
Published: January 2006

A 36‐year follow‐up on the original patient described with methylmalonic aciduria has shown that she has methylmalonyl‐CoA apomutase deficiency. The main clinical problem associated with her methylmalonic aciduria is progressive renal impairment requiring commencement of haemodialysis at 42 years of age.
Phenotypic study on total and partial lifetime traits for dairy ewes
Authors: El-Saied Usama M , de la Fuente L Fernando , Primitivo Fermín San
Published: January 2006

A data file on 36396 lactations was used to determine the strength of the phenotypic relationship between productive, reproductive and lifespan traits for 7935 Spanish Churra ewes. These ewes first lambed between 1989 and 1997 and belonged to 23 flocks. The study took into account four lifespan traits (lifetime, productive life, useful life and lifetime score), three productive traits (total milk yield produced during lifetime, lambs weaned during ewe lifetime and total revenues from sold milk and weaned lambs during lifetime) and two reproductive traits (age at first lambing and mean interval between successive lambings). Moreover, milk yield and revenues from sold milk and weaned lambs were calculated per day of lifetime, productive life and useful life. Partial lifespan traits were considered for the first three parities. The model included flock, birth year within flock and season of birth of the ewe as fixed effects. The first two effects contributed significantly to variation in all traits, while season significantly affected lifespan traits, productive traits and age at first lambing. Milk production level was added to the model for lifespan traits only. It significantly contributed to explaining the variation in all lifespan traits with high percentage of variance explained averaging 14·91%. Lifetime averaged 2324 d. Productive life accounted for 57% of lifetime while useful life represented 50% of productive life. Age at first lambing averaged 622 d and average days dry during lifetime was 560. During lifetime, ewes gave an average of 4·6 parities, 6·5 weaned lambs and 636 l of milk. Average revenue from milk and lambs during lifetime was €673. Milk/day of lifetime, productive life and useful life averaged 0·26, 0·51 and 0·93 l, respectively. The corresponding per-day revenues from sold milk and weaned lambs were, €0.27, €0.55 and €1.01, respectively. Lifespan and productive traits had strong relationships (rp among these traits ranged between 0·75 and 0·95). Two-parity and three-parity per-day milk yield had moderately high correlation (0·70–0·83) with total lifetime per-day milk yield traits. Therefore, good use of these traits would be helpful in determining best individuals early in life.
Accuracy of simplified sampling procedures for estimating milk composition in dairy ewes
Authors: Othmane M Houcine , Angel Fuertes J , Gonzalo Carlos , De La Fuente L Fernando , Primitivo Fermín San
Published: January 2006

Simplified designs of milk-composition recording, based on information from a single monthly milking, adjusted or not for interval between milkings and for milk yield, were simulated and evaluated for 2553 ewe-test-day records belonging to 155 lactations of Churra dairy ewes. Accuracy of simplified methods was evaluated by comparing estimated trait values (fat, protein, casein and total solid yields) with those observed both in a reference plan, where the two daily milkings were recorded at weekly intervals (A1), and in the official A4 milk recording (monthly records of the two daily milkings). Trait yields per lactation were estimated and adjusted to the only milking period (days in milk 30–120). Estimates of milk component traits were less precise when monthly designs, including the A4 design, were compared with a weekly sampling of both a.m. and p.m. milkings, with fat yield being the most difficult trait to estimate. All options with one daily milking every month were more accurate when the corresponding plan was based on, or began with, the a.m. milking. Adjustment for the preceding interval between milkings or milk yield did not improve sampling accuracy. The design alternating a.m. and p.m. milkings every month, without adjustment, is suggested for recoding milk component traits in dairy ewes.
The occurrence and nature of electrochemical activity in milk from a herd of dairy cows
Authors: Brain Jarod , Collier Wendy , Hart Alan
Published: January 2006

Amperometric sensors may be used in milk analysis but electrochemical interference from compounds other than the analyte is an on-going problem. A survey was made of the level of electrochemical activity (potential interference) in milk from a herd of dairy cows grazing on summer pasture. It was a ubiquitous feature of the aqueous phase of whey and de-proteinized milk over about 3 months. The nature of the interference was studied by differential pulse voltammetry and responses to ascorbic acid oxidase and uricase. The principal source of interference appeared to be uric acid.
Domestic and travel-related foodborne gastrointestinal illness in a population health survey
Authors: EVANS M. R. , SARVOTHAM T. , THOMAS D. R. , HOWARD A. J.
Published: January 2006

Routine surveillance data underestimate incidence of foodborne gastrointestinal (FGI) illness and provide little information on illness related to travel. We analysed data from the Welsh Health Survey to estimate population incidence, and to examine risk factors for FGI and factors associated with consulting a doctor. Reported frequency of any FGI in the 3 months before interview was 20·0% [95% confidence interval (CI) 19·5–20·4; equivalent to 0·8 episodes per person-year], and for travel-related FGI was 1·6% (95% CI 1·5–1·8). In the final model, sex, age group, marital status, self-reported health, long-term illness, smoking and alcohol consumption were all independent predictors of FGI. People who consulted a doctor were likely to be older, in poorer health, taking regular medication, or to report mental illness. FGI is common but risk factors for illness and consultation differ and impressions of the epidemiology of the disease based on surveillance data are therefore distorted.
How much can part-of-speech tagging help parsing?
Authors: DALRYMPLE MARY
Published: January 2006

Folk wisdom holds that incorporating a part-of-speech tagger into a system that performs deep linguistic analysis will improve the speed and accuracy of the system. Previous studies of tagging have tested this belief by incorporating an existing tagger into a parsing system and observing the effect on the speed of the parser and accuracy of the results. However, not much work has been done to determine in a fine-grained manner exactly how much tagging can help to disambiguate or reduce ambiguity in parser output. We take a new approach to this issue by examining the full parse-forest output of a large-scale LFG-based English grammar (Riezler et al. (2002)) running on the XLE grammar development platform (Maxwell and Kaplan (1993); Maxwell and Kaplan (1996)); and partitioning the parse outputs into equivalence classes based on the tag sequences for each parse. If we find a large number of tag-sequence equivalence classes for each sentence, we can conclude that different parses tend to be distinguished by their tags; a small number means that tagging would not help much in reducing ambiguity. In this way, we can determine how much tagging would help us in the best case, if we had the “perfect tagger” to give us the correct tag sequence for each sentence. We show that if a perfect tagger were available, a reduction in ambiguity of about 50% would be available. Somewhat surprisingly, about 30% of the sentences in the corpus that was examined would not be disambiguated, even by the perfect tagger, since all of the parses for these sentences shared the same tag sequence. Our study also helps to inform research on tagging by providing a targeted determination of exactly which tags can help the most in disambiguation.
Accumulation mode aerosol, pockets of open cells, and particle nucleation in the remote subtropical Pacific marine boundary layer
Authors: Petters Markus D. , Snider Jefferson R. , Stevens Bjorn , Vali Gabor , Faloona Ian , Russell Lynn M.
Published: January 2006

We analyze a marine boundary layer cloud field encountered during the second research flight of the second Dynamics and Chemistry of Marine Stratocumulus Experiment. The cloud field is distinguished by the presence of pockets of open cells. Differences between the pockets and the surrounding stratocumulus clouds are studied utilizing in situ and satellite data. The pockets are characterized as regions where cloud radar echo tops are unusually variable, accumulation mode aerosol concentrations are low, and Aitken mode particles with a mode diameter at 0.02 μm dominate aerosol number concentration. The Aitken mode particles are thought to be generated by a nucleation event which occurred within the marine boundary layer. The low accumulation mode concentrations associated with the pockets are proposed to be necessary for their maintenance.
Anomalous tilt of Isidis Planitia, Mars
Authors: McGowan Eileen M. , McGill George E.
Published: January 2006

We examine several models to account for the contrast between the global northern tilt of Mars and the southwest slope of Isidis Planitia and the putative Deuteronilus shoreline surrounding Isidis Planitia. We found the most probable cause for both the tilt of Isidis Planitia and the Deuteronilus shoreline at this location to be a peripheral bulge created by a load in Utopia basin. Using a flexural model it was found that a 12km load resulting in a 6 km deflection in Utopia basin could create a peripheral bulge that in distance and magnitude resembles the topographic profile from Isidis Planitia northeastward into Utopia basin.
On the use of a deep pressure gradient constraint for estimating the steady state ocean circulation from hydrographic data
Authors: Sidorenko D. , Danilov S. , Kivman G. , Schröter J.
Published: January 2006

Estimating unobserved quantities such as velocities and transports indirectly from temperature and salinity measurements is one of the best studied problems in physical oceanography. It is ill posed. The ill posedness is traditionally removed by adding prior information such as a level of no motion or a set of conservation principles. We propose to use the deep pressure gradient taken from a prognostic integration of an ocean general circulation model in primitive equations as a weak constraint when using the stationary inverse of the same model to derive transports. First results for the western boundary currents in the North Atlantic compare well with previous estimates from several studies including direct measurements.
Simulation study of a positive ionospheric storm phase observed at Millstone Hill
Authors: Swisdak M. , Huba J. D. , Joyce G. , Huang Chao‐Song
Published: January 2006

Simulation results from the NRL ionospheric model SAMI2 indicate that the changes in the F‐region over Millstone Hill during the geomagnetic storm beginning on 3 April 2004 are primarily due to the influence of a long‐lasting eastward electric field, as was previously suggested by C. Huang et al. [2005]. A simulation of the storm day agrees well with the observational data and shows that, compared with the ionosphere of the previous quiet day, the peak electron density in the F‐region (NmF2) increased by a factor of ≈2, the altitude of the peak density (hmF2) rose by ≈80 km, and the F‐region electron temperature decreased by ≈1000 K. Further simulations in which either the neutral atmosphere and winds or the electric field were replaced by their quiet day counterparts clearly suggest that the electric field played the dominant, although not exclusive, role in producing these effects.
Combined valence bond-molecular mechanics potential-energy surface and direct dynamics study of rate constants and kinetic isotope effects for the H+C2H6 reaction
Authors: Chakraborty Arindam , Zhao Yan , Lin Hai , Truhlar Donald G.
Published: January 2006

This article presents a multifaceted study of the reaction H+C2H6→H2+C2H5 and three of its deuterium-substituted isotopologs. First we present high-level electronic structure calculations by the W1, G3SX, MCG3-MPWB, CBS-APNO, and MC-QCISD/3 methods that lead to a best estimate of the barrier height of 11.8±0.5kcal∕mol. Then we obtain a specific reaction parameter for the MPW density functional in order that it reproduces the best estimate of the barrier height; this yields the MPW54 functional. The MPW54 functional, as well as the MPW60 functional that was previously parametrized for the H+CH4 reaction, is used with canonical variational theory with small-curvature tunneling to calculate the rate constants for all four ethane reactions from 200 to 2000 K. The final MPW54 calculations are based on curvilinear-coordinate generalized-normal-mode analysis along the reaction path, and they include scaled frequencies and an anharmonic C–C bond torsion. They agree with experiment within 31% for 467–826 K except for a 38% deviation at 748 K; the results for the isotopologs are predictions since these rate constants have never been measured. The kinetic isotope effects (KIEs) are analyzed to reveal the contributions from subsets of vibrational partition functions and from tunneling, which conspire to yield a nonmonotonic temperature dependence for one of the KIEs. The stationary points and reaction-path potential of the MPW54 potential-energy surface are then used to parametrize a new kind of analytical potential-energy surface that combines a semiempirical valence bond formalism for the reactive part of the molecule with a standard molecular mechanics force field for the rest; this may be considered to be either an extension of molecular mechanics to treat a reactive potential-energy surface or a new kind of combined quantum-mechanical/molecular mechanical (QM/MM) method in which the QM part is semiempirical valence bond theory; that is, the new potential-energy surface is a combined valence bond molecular mechanics (CVBMM) surface. Rate constants calculated with the CVBMM surface agree with the MPW54 rate constants within 12% for 534–2000 K and within 23% for 200–491 K. The full CVBMM potential-energy surface is now available for use in variety of dynamics calculations, and it provides a prototype for developing CVBMM potential-energy surfaces for other reactions.
The frequency-dependent dipole polarizability of the mercury dimer from four-component relativistic density-functional theory
Authors: Gaston Nicola , Schwerdtfeger Peter , Saue Trond , Greif Jörn
Published: January 2006

The frequency-dependent dipole polarizability of Hg2 is calculated using response theory within four-component relativistic density-functional theory [using the local-density approximation (LDA) and the hybrid functional B3LYP] including corrections for the basis-set superposition error. The anisotropic component of the polarizability tensor agrees well with the values obtained from collision-induced Raman spectroscopy carried out at a wavelength of 488nm. The values obtained from the two density functionals agree closely with the experimentally derived anisotropy component of the dipole polarizability, despite their rather large differences in the dimer potential-energy curves (LDA is strongly overbinding while B3LYP is purely repulsive). The first two refractivity virial coefficients for the generalized Clausius-Mossotti function are derived.
Broadband dielectric study of the glass transition in poly(ethyleneglycol)-water mixture
Authors: Sudo S. , Shimomura M. , Kanari K. , Shinyashiki N. , Yagihara S.
Published: January 2006

We performed broadband dielectric measurements of a polyethyleneglycol-water mixture in the frequency range between 10GHz and 1μHz and the temperature range between 300 and 133K. One relaxation process is observed throughout the whole temperature range. The temperature dependence of the relaxation time clearly obeys the Vogel-Fulcher law above 183K, and the Arrhenius law below 183K. This observed relaxation process is the secondary process, and the primary process related to the glass transition is masked by the low-frequency ionic contribution below 183K. The glass transition concerned with the masked primary process leads to the Vogel-Fulcher to Arrhenius transition of the secondary process.
The importance of hydrogen’s potential-energy surface and the strength of the forming R–H bond in surface hydrogenation reactions
Authors: Crawford Paul , Hu P.
Published: January 2006

An understanding of surface hydrogenation reactivity is a prevailing issue in chemistry and vital to the rational design of future catalysts. In this density-functional theory study, we address hydrogenation reactivity by examining the reaction pathways for N+H→NH and NH+H→NH2 over the close-packed surfaces of the 4d transition metals from Zr–Pd. It is found that the minimum-energy reaction pathway is dictated by the ease with which H can relocate between hollow-site and top-site adsorption geometries. A transition state where H is close to a top site reduces the instability associated with bond sharing of metal atoms by H and N (NH) (bonding competition). However, if the energy difference between hollow-site and top-site adsorption energies (ΔEH) is large this type of transition state is unfavorable. Thus we have determined that hydrogenation reactivity is primarily controlled by the potential-energy surface of H on the metal, which is approximated by ΔEH, and that the strength of N (NH) chemisorption energy is of less importance. ΔEH has also enabled us to make predictions regarding the structure sensitivity of these reactions. Furthermore, we have found that the degree of bonding competition at the transition state is responsible for the trend in reaction barriers (Ea) across the transition series. When this effect is quantified a very good linear correlation is found with Ea. In addition, we find that when considering a particular type of reaction pathway, a good linear correlation is found between the destabilizing effects of bonding competition at the transition state and the strength of the forming N–H (HN–H) bond.
Phoretic forces on convex particles from kinetic theory and nonequilibrium thermodynamics
Authors: Hütter Markus , Kröger Martin
Published: January 2006

In this article we derive the phoretic forces acting on a tracer particle, which is assumed to be small compared to the mean free path of the surrounding nonequilibrium gas, but large compared to the size of the surrounding gas molecules. First, we review and extend the calculations of Waldmann [Z. Naturforsch. A 14A, 589 (1959)] using half-sphere integrations and an accommodation coefficient characterizing the collision process. The presented methodology is applied to a gas subject to temperature, pressure, and velocity gradients. Corresponding thermophoretic, barophoretic, and rheophoretic forces are derived, and explicit expressions for spherical particles are compared to known results. Second, nonequilibrium thermodynamics is used to join the diffusion equation for the tracer particle with the continuum equations of nonisothermal hydrodynamics of the solvent. So doing, the distinct origin of the thermophoretic and barophoretic forces is demonstrated. While the latter enters similarly to an interaction potential, the former is given by flux-flux correlations in terms of a Green-Kubo relation, as shown in detail.
Entanglement monotones for multi-qubit states based on geometric invariant theory
Authors: Heydari Hoshang
Published: January 2006

We construct entanglement monotones for multi-qubit states based on Plücker coordinate equations of Grassmann variety, which are a central notion in geometric invariant theory. As an illustrative example, we in detail investigate entanglement monotones of a three-qubit state.
Influence of the surrounding host in obtaining tunable and strong visible photoluminescence from silicon nanoparticles
Authors: Santana G. , Monroy B. M. , Ortiz A. , Huerta L. , Alonso J. C. , Fandiño J. , Aguilar-Hernández J. , Hoyos E. , Cruz-Gandarilla F. , Contreras-Puentes G.
Published: January 2006

We have investigated the influence of the microstructure and chemistry of the surrounding host on the strong visible photoluminescence (PL) from silicon nanoclusters (nc-Si) embedded in three different silicon-based dielectric compounds: SixNy:H,Cl, SixNyOz:H,Cl, and SixOz:H,Cl, obtained from silicon nitride films deposited by SiH2Cl2∕NH3∕H2 plasma-enhanced chemical vapor deposition at different growth pressures. A blueshift is found in the PL coming from the nc-Si as the content of oxygen in the surrounding host is increased, and a significant improvement in PL intensity is achieved when the nc-Si are well passivated with O instead of H. We discuss the PL behavior in terms of the quantum confinement model and passivation state of the nc-Si surface.
Formation and activation energy of CdxZn1−xTe nanostructures with different dimensions grown on ZnTe buffer layers
Authors: Kim T. W. , Lee H. S. , Park H. L.
Published: January 2006

Atomic force microscopy (AFM) and photoluminescence (PL) measurements were carried out to investigate the formation process and the activation energy of different-dimensional CdxZn1−xTe∕ZnTe nanostructures. The results of the AFM images show that CdxZn1−xTe quantum dots (QDs) are formed and that the dimensional transformation from CdxZn1−xTe QDs to CdxZn1−xTe quantum wires is caused by coalescence. The excitonic peak corresponding to the transition from the ground electronic subband to the ground heavy-hole transitions in CdxZn1−xTe∕ZnTe nanostructures shifts to lower energy with increasing thickness of the CdxZn1−xTe layer due to variations in the thickness and the dimension of the layer. The activation energy of the electrons confined in the CdxZn1−xTe∕ZnTe nanostructures, as obtained from the temperature-dependent PL spectra, was significantly affected by the thickness and the dimension of the CdxZn1−xTe layer.
Computation of recurrent minimal genomic alterations from array-CGH data
Authors: Rouveirol C. , Stransky N. , Hupé Ph. , Rosa Ph. La , Viara E. , Barillot E. , Radvanyi F.
Published: January 2006

Motivation: The identification of recurrent genomic alterations can provide insight into the initiation and progression of genetic diseases, such as cancer. Array-CGH can identify chromosomal regions that have been gained or lost, with a resolution of ∼1 mb, for the cutting-edge techniques. The extraction of discrete profiles from raw array-CGH data has been studied extensively, but subsequent steps in the analysis require flexible, efficient algorithms, particularly if the number of available profiles exceeds a few tens or the number of array probes exceeds a few thousands.

Results: We propose two algorithms for computing minimal and minimal constrained regions of gain and loss from discretized CGH profiles. The second of these algorithms can handle additional constraints describing relevant regions of copy number change. We have validated these algorithms on two public array-CGH datasets.

Availability: From the authors, upon request.

Contact:  celine@lri.fr

Supplementary information: Supplementary data are available at Bioinformatics online.
Discontinuous epitope prediction based on mimotope analysis
Authors: Moreau Violaine , Granier Claude , Villard Sylvie , Laune Daniel , Molina Franck
Published: January 2006

Motivation: Phage display is a widespread technique used to obtain peptide mimotopes selected by binding to a given monoclonal antibody in a similar way as the native epitope. However, the localization of the interaction site mimicked by the mimotopes on the surface of the antigen is not always a straightforward task. MIMOP is a computational tool developed with the aim of helping experimentalists to analyze a set of mimotope sequences and guide them in the identification of the mimicked region.

Results: To predict potential epitopic regions, MIMOP integrates two different approaches combining two- and three-dimensional analyses: MimAlign starts from degenerated alignment analyses, and MimCons is based on consensus identification. The relevance and usefulness of the tool are illustrated by four use cases corresponding to real-life situations.

Availability: upon request.

Contact:  franck.molina@cpbs.univ-montp1.fr
Novel technique for preprocessing high dimensional time-course data from DNA microarray: mathematical model-based clustering
Authors: Hakamada Kazumi , Okamoto Masahiro , Hanai Taizo
Published: January 2006

Motivation. Classifying genes into clusters depending on their expression profiles is one of the most important analysis techniques for microarray data. Because temporal gene expression profiles are indicative of the dynamic functional properties of genes, the application of clustering analysis to time-course data allows the more precise division of genes into functional classes. Conventional clustering methods treat the sampling data at each time point as data obtained under different experimental conditions without considering the continuity of time-course data between time periods t and t +1. Here, we propose a method designated mathematical model-based clustering (MMBC).

Results: The proposed method, designated MMBC, was applied to artificial data and time-course data obtained using Saccharomyces cerevisiae. Our method is able to divide data into clusters more accurately and coherently than conventional clustering methods. Furthermore, MMBC is more tolerant to noise than conventional clustering methods.

Availability: Software is available upon request.

Contact:  taizo@brs.kyushu-u.ac.jp
Metagenomic analysis of mesopelagic Antarctic plankton reveals a novel deltaproteobacterial group
Authors: Moreira David , Rodríguez-Valera Francisco , López-García Purificación
Published: January 2006

Phylogenetic screening of 3200 clones from a metagenomic library of Antarctic mesopelagic picoplankton allowed the identification of two bacterial 16S-rDNA-containing clones belonging to the Deltaproteobacteria, DeepAnt-1F12 and DeepAnt-32C6. These clones were very divergent, forming a monophyletic cluster with the environmental sequence GR-WP33-58 that branched at the base of the myxobacteria. Except for the possession of complete rrn operons without associated tRNA genes, DeepAnt-1F12 and DeepAnt-32C6 were very different in gene content and organization. Gene density was much higher in DeepAnt-32C6, whereas nearly one-third of DeepAnt-1F12 corresponded to intergenic regions. Many of the predicted genes encoded by these metagenomic clones were informational (i.e. involved in replication, transcription, translation and related processes). Despite this, a few putative cases of horizontal gene transfer were detected, including a transposase. DeepAnt-1F12 contained one putative gene encoding a long cysteine-rich protein, probably membrane-bound and Ca2+-binding, with only eukaryotic homologues. DeepAnt-32C6 carried some predicted genes involved in metabolic pathways that suggested this organism may be anaerobic and able to ferment and to degrade complex compounds extracellularly.