bluuebunny/crossref_metadata_2025 huggingface dataset:
BRMS1 transcriptional repression correlates with CpG island methylation and advanced pathological stage in non‐small cell lung cancer
Authors: Nagji Alykhan S , Liu Yuan , Stelow Edward B , Stukenborg George J , Jones David R
Published: March 2010

Breast cancer metastasis suppressor gene‐1 (BRMS1) mRNA and protein expression are significantly decreased in non‐small cell lung cancer (NSCLC) and this is a poor prognostic indicator. Given that the BRMS1 promoter region contains a promoter‐associated CpG island (CGI) that encompasses the transcriptional start site, we hypothesized that decreased BRMS1 mRNA and protein levels in NSCLC was secondary to increased BRMS1 promoter methylation. Methylation‐specific PCR (MSP) of the two known CGIs (−3477 to − 2214 and − 531 to + 608) in the BRMS1 genome was performed in NSCLC cells. This demonstrated a robust increase in methylation of the promoter‐associated CGI (−531 to + 608) but not of the upstream CGI (−3477 to − 2214). To experimentally verify that methylation contributes to BRMS1 transcriptional repression, we cloned the BRMS1 promoter region, including the promoter‐associated CGI, into a luciferase reporter gene and found that BRMS1 promoter activity was dramatically inhibited under methylated conditions. We then assessed the BRMS1 methylation profile with MSP and bisulphite‐sequencing PCR in human NSCLC adenocarcinoma (n = 20) and squamous cell carcinoma (n = 20) relative to adjacent non‐cancerous bronchial epithelium. There was a significant increase in BRMS1 promoter methylation in all NSCLC specimens relative to non‐cancerous tissues, with the most dramatic difference in squamous cell cancer histology. Subsequent immunostaining demonstrated that nuclear BRMS1 expression is reduced in lung cancer specimens compared to normal bronchial epithelium. The association between BRMS1 promoter methylation and specific clinical and histopathological variables was examined using a general linear model. Pathological tumour stage was associated with increased BRMS1 methylation in squamous cell cancers. These observations demonstrate that methylation of the promoter‐associated CGI in BRMS1 results in its transcriptional repression, and highlight the potential clinical relevance of this methylation event with respect to NSCLC tumour histology and pathological stage. Copyright © 2010 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Curing of styrene‐free unsaturated polyester alkyd: synthesis, characterization and simulation
Authors: Mironi‐Harpaz Iris , Alperstein David , Knani Dafna , Narkis Moshe
Published: March 2010

Experimental and simulation studies of the crosslinking process of styrene‐free unsaturated polyester (UP) alkyd chains are presented. The thermal and mechanical properties of the crosslinked UP alkyd are studied as a function of the peroxide concentration. The characterized and simulated thermoset matrix properties are compared. Simulation of the crosslinking reaction is used to improve the understanding of the process and to define the species involved in it. The main experimental characterization tools used were differential scanning calorimetry and dynamic mechanical analysis. The main simulation tools used were a Monte Carlo procedure for the crosslinking process and a density functional theory‐based quantum code for the scission process. Good agreement between the experimental and simulation results was achieved. Copyright © 2010 Society of Chemical Industry
Synthesis and fluorescence properties of novel 1,10‐phenanthroline‐functionalized polyaryletherketone and its rare earth complexes
Authors: Liu Dan , Yu Hao , Wang Zhonggang , Nie Qiuping
Published: March 2010

1,10‐Phenanthroline‐functionalized polyaryletherketone (PPEK) was synthesized by the amidation reaction of 5‐amino‐1,10‐phenanthroline with polyaryletherketone containing pendant acyl chloride groups. Subsequently, a series of novel rare earth coordination polymers (with rare earths Eu3+, Tb3+, Sm3+ and Dy3+) were prepared, using PPEK as macromolecular ligand and the small 1,10‐phenanthroline (Phen) molecule as synergistic ligand. Their structures were characterized using Fourier transform infrared spectroscopy, elemental analysis and X‐ray diffraction, which confirmed that both PPEK and Phen participated in the coordination reaction with the rare earth ions, and that the rare earth ions could disperse homogeneously in the polymer matrix. The rare earth coordination polymers were soluble in polar solvents such as N,N‐dimethylformamide, N,N‐dimethylacetamide and N‐methylpyrrolidone, and could be easily cast into transparent tough thin films. Fluorescence measurements indicated that all the coordination polymers exhibited the intense characteristic fluorescence of the corresponding rare earth ions under ultraviolet excitation, showing their application potential in optical display devices. Copyright © 2010 Society of Chemical Industry
Evidence‐based early reading practices within a Response to Intervention system
Authors: Bursuck Bill , Blanks Brooke
Published: March 2010

Many students who experience reading failure are inappropriately placed in special education. A promising response to reducing reading failure and the overidentification of students for special education is Response to Intervention (RTI), a comprehensive early detection and prevention system that allows teachers to identify and support struggling readers early, before they fail. A key component of RTI is the implementation of evidence‐based reading practices within a multitiered framework. School psychologists are increasingly being asked to lead or be members of RTI building teams. As such, they can play an important role in assuring that evidence‐based practices in reading are implemented with integrity. The purpose of this article is to provide a framework for judging the extent to which early reading instruction within a multitier RTI system is evidence based. Key evidence‐based practices related to the content, design, and delivery of early reading instruction are described. © 2010 Wiley Periodicals, Inc.
The development of phonological awareness with specific language‐impaired and typical children
Authors: Thatcher Karen L.
Published: March 2010

This study investigated kindergarten, preschool, and first‐grade children who were typical or specific language impaired (SLI) to determine whether there were developmental differences in their phonological awareness abilities (i.e., syllable, onset/rime, phonemes). Results revealed a significant difference between children who were typical and children who were SLI on the sound‐segmentation tasks. The children who were typical were more effective at segmenting than were children who were SLI. Significant differences were also noted between the types of phonological task completed among participants. The combined data from this study revealed developmental trends in phonological awareness for the typical population. The developmental trend was not observed in the SLI population, however. Clinical implications are suggested. © 2010 Wiley Periodicals, Inc.
The terminal 5′ phosphate and proximate phosphorothioate promote ligation‐independent cloning
Authors: Liu Xi‐Peng , Liu Jian‐Hua
Published: March 2010

Function studies of many proteins are waited to develop after genome sequencing. High‐throughout technology of gene cloning will strongly promote proteins' function studies. Here we describe a ligation‐independent cloning (LIC) method, which is based on the amplification of target gene and linear vector by PCR using phosphorothioate‐modified primers and the digestion of PCR products by λ exonuclease. The phosphorothioate inhibits the digestion and results in the generation of 3′ overhangs, which are designed to form complementary double‐stranded DNA between target gene and linear vector. We compared our phosphorothioate primer cloning methods with several LIC methods, including dU primer cloning, hybridization cloning, T4 DNA polymerase cloning, and in vivo recombination cloning. The cloning efficiency of these LIC methods are as follows: phosphorothioate primer cloning > dU primer cloning > hybridization cloning > T4 DNA polymerase cloning >> in vivo recombination cloning. Our result shows that the 3′ overhangs is a better cohesive end for LIC than 5′ overhang and the existence of 5′phosphate promotes DNA repair in Escherichia coli, resulting in the improvement of cloning efficiency of LIC. We succeeded in constructing 156 expression plasmids of Aeropyrum pernix genes within a week using our method.
Structural and functional analysis of the phosphoryl transfer reaction mediated by the human small C‐terminal domain phosphatase, Scp1
Authors: Zhang Mengmeng , Liu June , Kim Youngjun , Dixon Jack E. , Pfaff Samuel L. , Gill Gordon N. , Noel Joseph P. , Zhang Yan
Published: March 2010

Human small C‐terminal domain phosphatase 1 (Scp1) modulates the phosphorylation state of the C‐terminal domain (CTD) of eukaryotic RNA polymerase II (RNAP II), with preference for phosphorylated Ser5 in the tandem heptad repeats of the CTD. Additionally, Scp1 was identified as a conserved regulator of neuronal stem cell development. Scp1 is a member of haloacid dehalogenase (HAD) superfamily, whose catalysis depends on a Mg2+ ion and a DXDX(T/V) motif. The first Asp of the motif is identified as the nucleophile that is subject to phosphorylation leading to a phosphoryl‐aspartate intermediate. This high‐energy mixed anhydride intermediate is subsequently hydrolyzed to regenerate the enzyme. In the present study, we successfully captured the phosphoryl‐aspartate intermediate in the crystal structure of a Scp1D206A mutant soaked with para‐nitrophenyl phosphate (pNPP), providing strong evidence for the proposed mechanism. Furthermore, steady‐state kinetic analysis of a variety of Scp1 mutants revealed the importance of Asp206 in Mg2+ coordination mediated by a water molecule. Overall, we captured the snapshots of the phosphoryl transfer reaction at each stage of Scp1‐mediated catalysis. Through structural‐based sequence alignment, we show that the spatial position of the D206 side chain is strictly conserved throughout HAD family. Our results strongly suggest that Asp206 and its equivalent residues in other HAD family members play important structural and possible mechanistic roles.
On the use of structural templates for high‐resolution docking
Authors: Movshovitz‐Attias Dana , London Nir , Schueler‐Furman Ora
Published: March 2010

Reliable high‐resolution prediction of protein complex structures starting from the free monomers is a considerable challenge toward large‐scale mapping of the structural details of protein‐protein interactions. The current major bottleneck is to model the conformational changes of the monomer backbone upon binding. We evaluate the use of homolog structures as source for conformational diversity, within the framework of RosettaDock—a leading high‐resolution docking protocol. We find that the use of homolog templates can improve significantly the modeling of a complex structure, including known difficult cases. Several conformational changes however are not sampled by any of the templates, indicating the need for additional sources of conformational variability. Interestingly, the successful homolog templates are not restricted to a confined range of sequence identity, highlighting the importance of the backbone conformation rather than the sequence. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Polyglutamine fibrils are formed using a simple designed β‐hairpin model
Authors: Smith Melanie H. , Miles Timothy F. , Sheehan Molly , Alfieri Katherine N. , Kokona Bashkim , Fairman Robert
Published: March 2010

Polyglutamine repeats are found in proteins associated with many neurodegenerative diseases. These repeats are responsible for intracellular protein aggregation that resemble amyloid plaques and contain the hallmarks of cross‐β fibrillar structures. Recent work has suggested that the glutamines are involved in aggregation through two possible mechanisms: one involving only side‐chain hydrogen bonding and a second involving interdigitation of the glutamines with tight van der Waal's packing (steric zipper model). We are interested in determining which interactions are particularly involved in early assembly processes and have developed a β‐hairpin model system to address this problem. Our model system is designed to stabilize a putative high‐energy nucleating structure to provide a window to view early assembly processes. We have applied spectroscopy tools (circular dichroism, infrared, and dynamic light scattering) to probe the self‐assembly of β‐sheet fibrils. These experiments established the conditions to study fibrillar morphology using atomic force microscopy. We show that fibrils are short with minimal lateral growth, suggesting that this may be a good model system for studying early assembly steps. Proteins 2010. © 2010 Wiley‐Liss, Inc.
A localization technique for ensemble Kalman filters
Authors: Bergemann Kay , Reich Sebastian
Published: March 2010

Ensemble Kalman filter techniques are widely used to assimilate observations into dynamical models. The phase‐space dimension is typically much larger than the number of ensemble members, which leads to inaccurate results in the computed covariance matrices. These inaccuracies can lead, among other things, to spurious long‐range correlations, which can be eliminated by Schur‐product‐based localization techniques. In this article, we propose a new technique for implementing such localization techniques within the class of ensemble transform/square‐root Kalman filters. Our approach relies on a continuous embedding of the Kalman filter update for the ensemble members, i.e. we state an ordinary differential equation (ODE) with solutions that, over a unit time interval, are equivalent to the Kalman filter update. The ODE formulation forms a gradient system with the observations as a cost functional. Besides localization, the new ODE ensemble formulation should also find useful application in the context of nonlinear observation operators and observations that arrive continuously in time. Copyright © 2010 Royal Meteorological Society
Thermal rate coefficients calculation for the H+ + LiH reaction
Authors: Da Cunha Wiliam Ferreira , Barreto Patricia R. P. , Silva Geraldo Magela E , Martins João B. L. , Gargano Ricardo
Published: March 2010

Transition State Theory, with Wigner tunneling correction, was employed to determine the thermal rate coefficients for the first excited state of the H+ + LiH reaction using the potential energy surface calculated and fitted by Martinazzo et al. [Martinazzo et al., J Chem Phys 2003, 119, 11241]. The calculated thermal rate coefficients, in the temperature range of 500–1,000 K, are near to the value of 10−9 cm3 s−1 and tend to a constant value (10−8 cm3 s−1) at lower temperatures (200 K). These results support the recent investigation of Bulut et al. that showed the TRC to be nearly independent of temperature. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Molecular excitation spectra by TDDFT with the nonadiabatic exact exchange kernel
Authors: Ipatov Andrey , Heßelmann Andreas , Görling Andreas
Published: March 2010

A time‐dependent density functional theory (TDDFT) method using the nonadiabatic exact‐exchange kernel is discussed. Compared to previous TDDFT methods with orbital‐dependent kernels, the presented time‐dependent exact exchange (TDEXX) approach avoids a numerical unstable inversion of the Kohn–Sham response function. If the complete frequency dependency of the exact‐exchange kernel is taken into account, then the proposed method yields the long‐range distance behavior of charge‐transfer (CT) excitation energies qualitatively correctly. The relation between time‐dependent Hartree–Fock and TDEXX approaches is analyzed. This analysis shows by formal arguments why the TDEXX method is capable to correctly treat CT excitations and conversely shows that the problems to describe CT excitations with conventional TDDFT methods based on generalized gradient approximations (GGAs) has its origin in the shortcomings of the GGA exchange functionals. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Distances between pairs of vertices and vertical profile in conditioned Galton–Watson trees
Authors: Devroye Luc , Janson Svante
Published: March 2010

We consider a conditioned Galton–Watson tree and prove an estimate of the number of pairs of vertices with a given distance, or, equivalently, the number of paths of a given length.

We give two proofs of this result, one probabilistic and the other using generating functions and singularity analysis.

Moreover, the latter proof yields a more general estimate for generating functions, which is used to prove a conjecture by Bousquet–Mélou and Janson (Bousquet‐Mélou and Janson, Ann Appl Probab 16 (2006) 1597–1632), saying that the vertical profile of a randomly labelled conditioned Galton–Watson tree converges in distribution, after suitable normalization, to the density of ISE (Integrated Superbrownian Excursion). © 2011 Wiley Periodicals, Inc. Random Struct. Alg., 38, 381–395, 2011
The ubiquitous Beilby layer on aluminium surfaces
Authors: Scamans G. M. , Frolish M. F. , Rainforth W. M. , Zhou Z. , Liu Y. , Zhou X. , Thompson G. E.
Published: March 2010

In 1996, it was found that the Beilby layer on rolled aluminium sheet could be imaged in the transmission electron microscope (TEM) on ultramicrotomed cross sections of the sheet surface. Following from this observation, we have examined Beilby layers on all types of aluminium surfaces that have been subject to high shear processing treatments such as rolling, grinding or machining. The layers are microcrystalline rather than amorphous, and they strongly influence properties like corrosion resistance and reflectance. Preferential precipitation in these deformed surface layers results in their electrochemical activation and it is responsible for the development of underfilm corrosion in most architectural and automotive alloys. More recently, it has been possible to directly image Beilby layers on ultramicrotomed stubs using the new generation of low kilovoltage high‐resolution scanning electron microscopes and to carry out high‐resolution TEM of sections cut from precisely located surface features. The paper presents an overview of all the recent investigations of high shear induced Beilby layers on aluminium alloys and discusses their control of surface properties. Copyright © 2010 John Wiley & Sons, Ltd.
Prospective external validation of the ‘ovarian crescent sign’ as a single ultrasound parameter to distinguish between benign and malignant adnexal pathology
Authors: Van Holsbeke C. , Van Belle V. , Leone F. P. G. , Guerriero S. , Paladini D. , Melis G. B. , Greggi S. , Fischerova D. , De Jonge E. , Neven P. , Bourne T. , Valentin L. , Van Huffel S. , Timmerman D.
Published: March 2010

Objective

To determine the sensitivity and specificity of the ‘ovarian crescent sign’ (OCS)—a rim of normal ovarian tissue seen adjacent to an ipsilateral adnexal mass—as a sonographic feature to discriminate between benign and malignant adnexal masses.

Methods

The patients included were a subgroup of patients participating in the International Ovarian Tumor Analysis (IOTA) Phase 2 study, which is an international multicenter study. The subgroup comprised 1938 patients, with an adnexal mass, recruited from 19 ultrasound centers in different countries. All patients were scanned using the same standardized ultrasound protocol. Information on more than 40 demographic and ultrasound variables were collected, but the evaluation of the OCS was optional. Only patients from centers that had evaluated the OCS in ≥ 90% of their cases were included. The gold standard was the histological diagnosis of the adnexal mass. The ability of the OCS to discriminate between borderline or invasively malignant vs. benign adnexal masses, as well as between invasively malignant vs. other (benign and borderline) tumors, was determined and compared with the performance of subjective evaluation of ultrasound findings by the ultrasound examiner.

Results

The OCS was evaluated in 1377 adnexal masses from 12 centers, 938 (68%) masses being benign, 86 (6%) borderline, 305 (22%) primary invasive and 48 (3%) metastases. The OCS was present in 398 (42%) of 938 benign masses, in 14 (16%) of 86 borderline tumors, in 18 (6%) of 305 primary invasive tumors (one malignant struma ovarii, one uterine clear cell adenocarcinoma and 16 epithelial carcinomas, i.e. four Stage I and 12 Stage II–IV) and in two (4%) of 48 ovarian metastases. Hence, the sensitivity and specificity for absent OCS to identify a malignancy was 92% and 42%, respectively, and the positive and negative likelihood ratios (LR+ and LR−, respectively) were 1.60 and 0.18. Subjective impression performed significantly better than the OCS. Sensitivity and specificity were 90% and 92%, respectively, LR+ was 11.0 and LR− was 0.10. For discrimination between invasive vs. benign or borderline tumors, the sensitivity for absent OCS was 94%, the specificity was 40%, the LR+ was 1.58 and the LR− was 0.14.

Conclusion

This study confirms previous reports that the presence of the OCS decreases the likelihood of invasive malignancy in adnexal masses. However it is a poor discriminator between benign and malignant adnexal masses. Copyright © 2010 ISUOG. Published by John Wiley & Sons, Ltd.
Security mechanism for voice over multipath mobilead hocnetworks
Authors: Vaidya Binod , Denko Mieso K. , Rodrigues Joel J. P. C.
Published: March 2010

In the next generation of wireless communication systems, there will be a need for the rapid deployment of independent mobile users for video and voice communication over wireless network. It can be seen that since the demand for Voice over IP (VoIP) over wireless network is growing, the use of VoIP over mobilead hocnetwork (MANET) is expected to grow as well. However, security is a critical issue in MANETs where mobile nodes communicate with each other over relatively unreliable wireless links without any preexisting infrastructure. In this paper, we present a framework for secure voice transmission over multipath MANET. An efficient traffic allocation approach for multipath MANET is proposed in order to deliver real‐time traffic over it. The proposed security mechanism was evaluated through two analyses. The correctness of the proposed mechanism was proved using Gong, Needham, and Yahalom (GNY) logic while the security analysis shows that the proposed scheme is resistant to various attacks. For the performance evaluation of the proposed framework, simulations were conducted and the results of the simulation experiments show that it is efficient and robust in terms of various performance metrics. Copyright © 2010 John Wiley & Sons, Ltd.
Bigram proximity matrix
Authors: Martinez Angel R.
Published: March 2010

A transformation of the text stream called a bigram proximity
matrix (BPM) has been developed. The BPM is used to encode free‐form text so computational techniques can be applied to this type of information resource. For example, one could classify the encoded documents using k nearest neighbor (k‐NN) discrimination, group the documents according to their topic, search for latent topics, and more. The hope is that encoding text documents using the BPM will preserve the meaning better than the bag‐of‐words method commonly used in information retrieval and is easier to execute than other natural language processing applications. In this article, we provide a brief introduction to natural language processing and definitions for some of the concepts. Next, we define the BPM and give some examples of how it has been used. We then provide a weighted variant of the BPM and conclude with extensions to this type of document encoding. Copyright © 2010 John Wiley & Sons, Inc.

This article is categorized under:

Statistical Learning and Exploratory Methods of the Data Sciences > Text Mining
Modeling of blood flow in arterial trees
Authors: Anor Tomer , Grinberg Leopold , Baek Hyoungsu , Madsen Joseph R. , Jayaraman Mahesh V. , Karniadakis George E.
Published: March 2010

Advances in computational methods and medical imaging techniques have enabled accurate simulations of subject‐specific blood flows at the level of individual blood cell and in complex arterial networks. While in the past, we were limited to simulations with one arterial bifurcation, the current state‐of‐the‐art is simulations of arterial networks consisting of hundreds of arteries. In this paper, we review the advances in methods for vascular flow simulations in large arterial trees. We discuss alternative approaches and validity of various assumptions often made to simplify the modeling. To highlight the similarities and discrepancies of data computed with different models, computationally intensive three‐dimensional (3D) and inexpensive one‐dimensional (1D) flow simulations in very large arterial networks are employed. Finally, we discuss the possibilities, challenges, and limitations of the computational methods for predicting outcomes of therapeutic interventions for individual patients. Copyright © 2010 John Wiley & Sons, Inc.

This article is categorized under:

Analytical and Computational Methods > Computational Methods

Models of Systems Properties and Processes > Organ, Tissue, and Physiological Models

Translational, Genomic, and Systems Medicine > Translational Medicine
Predation as a probable mechanism relating winter weather to population dynamics in a North American porcupine population
Authors: Mabille Géraldine , Descamps Sébastien , Berteaux Dominique
Published: March 2010

An abundance index of an eastern Quebec population of North American porcupines (Erethizon dorsatum) has cycled with superimposed periodicities of 11 and 22 years from 1868 to 2000. This cycle closely followed 11‐ and 22‐year cycles in solar irradiance and local weather (e.g., winter precipitation and spring temperature), generating the hypothesis that solar activity may affect porcupine abundance through effects on local weather. We investigated the mechanisms linking porcupine abundance to local weather conditions using a 6‐year study (2000–2005) involving individual mark‐recapture, radio tracking, seasonal survival analyses and identification of mortality causes. Summer (May–August) survival was high and constant over the study period, whereas winter (August–May) survival was lower and varied during the duration of our study. Variations in local winter precipitation explained 89% of the variation in winter survival. Porcupine predation rates appeared strongly related to snow conditions; 95% of depredated porcupines were killed when snow was covering the ground, and predation rates were higher in years with increased winter precipitation. Our data thus support the hypothesis that changes in predation rates under different snow conditions were the mechanism relating climate to porcupine population dynamics, via modifications of the local predator–prey interactions and impacts on porcupine winter survival. Our study adds to the growing body of evidence supporting an effect of climate on predator–prey processes. Also, it identifies one possible mechanism involved in the relationship between solar irradiance and porcupine population cycles observed at this study site over a 130‐year period.
Genetic determinants of immune-response to a polysaccharide vaccine for typhoid
Authors: Majumder Partha P. , Staats Herman F. , Sarkar-Roy Neeta , Varma Binuja , Ghosh Trina , Maiti Sujit , Narayanasamy K. , Whisnant Carol C. , Stephenson James L. , Wagener Diane K.
Published: March 2010

Differences in immunological response among vaccine recipients are determined both by their genetic differences and environmental factors. Knowledge of genetic determinants of immunological response to a vaccine can be used to design a vaccine that circumvents immunogenetic restrictions. The currently available vaccine for typhoid is a pure polysaccharide vaccine, immune response to which is T-cell independent. Little is known about whether genetic variation among vaccinees associates with variation in their antibody response to a polysaccharide vaccine. We conducted a study on 1,000 individuals resident in an area at high-risk for typhoid; vaccinated them with the typhoid vaccine, measured their antibody response to the vaccine, assayed >2,000 curated SNPs chosen from 283 genes that are known to participate in immune-response; and analyzed these data using a strategy to (a) minimize the statistical problems associated with testing of multiple hypotheses, and (b) internally cross-validate inferences, using a half-sample design, with little loss of statistical power. The first stage analysis, using the first half-sample, identified 54 SNPs in 43 genes to be significantly associated with immune response. In the second-stage, these inferences were cross-validated using the second half-sample. First-stage results of only 8 SNPs (out of 54) in 7 genes (out of 43) were cross-validated. We tested additional SNPs in these 7 genes, and found 8 more SNPs to be significantly associated. Haplotypes constructed with these SNPs in these 7 genes also showed significant association. These 7 genes areDEFB1,TLR1,IL1RL1,CTLA4,MAPK8,CD86andIL17D. The overall picture that has emerged from this study is that (a) immune response to polysaccharide antigens is qualitatively different from that to protein antigens, and (b) polymorphisms in genes involved in polysaccharide recognition, signal transduction, inhibition of T-cell proliferation, pro-inflammatory signaling and eventual production of antimicrobial peptides are associated with antibody response to the polysaccharide vaccine for typhoid.
Can children with spina bifida and muscular dystrophy participate in their own health status evaluations?
Authors: McLimont Susan C. , Owen Janice L. , Wright James G.
Published: March 2010

Background

The outcomes movement has emphasized the importance of the patient in evaluating treatment outcome. However, concern has been raised about the ability of children, particularly those with multisystem disease, to evaluate their disability.

Purpose

To determine whether children with spina bifida and muscular dystrophy and their parents agree when asked about the relative difficulty of daily activities and the severity of symptoms experienced by the child.

Methods

First, a list of symptoms and activity restrictions was generated from the literature, clinicians, and interviews with families with spina bifida and muscular dystrophy. Second, another group of parents and children with spina bifida (with hip dislocation or scoliosis) and with muscular dystrophy (with scoliosis), including those before and after surgery, independently rated the severity and importance of their objective and subjective complaints.

Results

The correlation between parents and their children was high for both objective (median Spearman's = 0.70; standard deviation [SD] = ±0.17; range = −0.05–1.00) and subjective (median Spearman's = 0.76; SD = ±0.14; range = 0.13–1.00) complaints, with an overall excellent level of agreement (Kappa = 0.75; 95% confidence interval [CI]: 0.73, 0.76).

Conclusion

Children with spina bifida and muscular dystrophy are capable of understanding and assessing their disability.
Attitudes toward Highly Skilled and Low-skilled Immigration: Evidence from a Survey Experiment
Authors: HAINMUELLER JENS , HISCOX MICHAEL J.
Published: March 2010

Past research has emphasized two critical economic concerns that appear to generate anti-immigrant sentiment among native citizens: concerns about labor market competition and concerns about the fiscal burden on public services. We provide direct tests of both models of attitude formation using an original survey experiment embedded in a nationwide U.S. survey. The labor market competition model predicts that natives will be most opposed to immigrants who have skill levels similar to their own. We find instead that both low-skilled and highly skilled natives strongly prefer highly skilled immigrants over low-skilled immigrants, and this preference is not decreasing in natives' skill levels. The fiscal burden model anticipates that rich natives oppose low-skilled immigration more than poor natives, and that this gap is larger in states with greater fiscal exposure (in terms of immigrant access to public services). We find instead that rich and poor natives are equally opposed to low-skilled immigration in general. In states with high fiscal exposure, poor (rich) natives are more (less) opposed to low-skilled immigration than they are elsewhere. This indicates that concerns among poor natives about constraints on welfare benefits as a result of immigration are more relevant than concerns among the rich about increased taxes. Overall the results suggest that economic self-interest, at least as currently theorized, does not explain voter attitudes toward immigration. The results are consistent with alternative arguments emphasizing noneconomic concerns associated with ethnocentrism or sociotropic considerations about how the local economy as a whole may be affected by immigration.
Take Five, a nutrition education intervention to increase fruit and vegetable intakes: impact on consumer choice and nutrient intakes
Authors: Cox David N. , Anderson Annie S. , Reynolds Joanna , McKellar Susan , Lean Michael E. J. , Mela David J.
Published: March 2010

This study reports results from a randomized controlled intervention trial, focusing on: (1) the identification of successful consumer strategies for increasing fruit and vegetable intakes to the recommended levels of more than five (80 g) portions per day and (2) impact on overall diet and nutrient intakes. Adult men and women (n170) fulfilling the main recruitment criterion of eating less than five fruit and vegetable portions per day but contemplating increasing intakes were recruited. Complete valid dietary data was provided by 101 intervention (fifty-nine estimated fruit and vegetable intakes, and forty-two simultaneous weighed total dietary and estimated fruit and vegetable intakes) and twenty-four control subjects (weighed total dietary intakes). Intervention advice included the specific association of high fruit and vegetable intake with reduced risk of disease, practicalities, and portion definition with a target intake of greater than five 80 g fruit and vegetable portions per day for 8 weeks. There were significant effects (P< 0·001) on weighed intakes of fruit and vegetables in the intervention group, rising from 324 (se 25) to 557 (se 31) g/d and reflected by validated portion measures at 8 weeks intervention. Successful strategies chosen by ‘achievers’ of the target intake (65% of subjects) were conventional (fruit as a snack, vegetables with main meals etc.) and favoured fruit. There were significant increases in percentage energy from carbohydrate (from sugars not starch), vitamin C, carotenes and NSP and there was a significant decrease in percentage energy from fat for subjects who had high fat intakes (> 35% energy) at baseline. Follow-up self-reported measures at 6 and 12 months indicated mean intakes of 4·5 and 4·6 defined portions/d respectively, suggesting some sustainable effect. In conclusion, the intervention led to significant increases in fruit and vegetable intakes largely via conventional eating habits, with some desirable effects on macro- and micronutrient intakes.
An Early Cretaceous vertebrate assemblage from the Cabao Formation of NW Libya
Authors: LE LOEUFF JEAN , MÉTAIS EDDY , DUTHEIL DIDIER B. , RUBINO JEAN LOUP , BUFFETAUT ERIC , LAFONT FRANÇOIS , CAVIN LIONEL , MOREAU FABRICE , TONG HAIYAN , BLANPIED CHRISTIAN , SBETA ALI
Published: March 2010

Fossil vertebrates from the Cabao Formation discovered in the area of Nalut in northwestern Libya include the hybodont sharkPriohybodus, the crocodilianSarcosuchus, an abelisaurid, a baryonichine spinosaurid and a large sauropod with spatulate teeth. The Cabao Formation may be Hauterivian to Barremian in age, although an earlier Berriasian to Valanginian age cannot be excluded. Its dinosaur assemblage is reminiscent of that of the El Rhaz and Tiouraren formations of Niger and strongly differs from both the Cenomanian assemblages of Morocco and Egypt and the Late Aptian to Albian fauna of Tunisia. Fossil vertebrates may be an important tool to establish the stratigraphical framework of the poorly dated Early Cretaceous continental deposits of Africa.
A primitive sauropodomorph from the upper Elliot Formation of Lesotho
Authors: KNOLL F.
Published: March 2010

A well-preserved, articulated dinosaur skeleton from southern Africa is described. The specimen comes from the upper Elliot Formation (?Hettangian) of Ha Ralekoala (Lesotho) and represents a new species:Ignavusaurus rachelisgenus et species nova. A cladistic analysis suggests thatIgnavusaurusis more derived thanThecodontosaurus–Pantydraco, but more primitive thanEfraasia.Ignavusaurusindeed shares a number of unambiguous synapomorphies with the taxa more derived thanThecodontosaurus–Pantydraco, such as a fully open acetabulum, but it is more plesiomorphic thanEfraasiaand more derived sauropodomorphs as shown by the evidence of, for instance, the distal extremity of its tibia that is is longer (cranio-caudally) than wide (latero-medially). The discovery ofIgnavusaurusincreases the known diversity of the early sauropodomorph fauna of the upper Elliot Formation, which stands as one of the richest horizons in the world in this respect.
Should we stop using tricyclic antidepressants in pregnancy?
Authors: Pariante C. M. , Seneviratne G. , Howard L.
Published: March 2010

A new Swedish study by Reis & Källén describes approximately 15 000 women (and their babies) that, between 1995 and 2007, reported the use of antidepressants, or were prescribed such drugs, during pregnancy. In this study, pregnancy and teratogenic outcomes after exposure to tricyclic antidepressants are, for most measures, equal or worse than after exposure to selective serotonin reuptake inhibitors or other antidepressants. Based on this and on a review of the few other studies available (admittedly, a relatively small number of women on which conclusions can be based), the authors of this Editorial challenge the ‘perinatal myth’ that tricyclics are the safest choice in pregnancy.
Memory and strategic processing in first-degree relatives of obsessive compulsive patients
Authors: Segalàs C. , Alonso P. , Real E. , Garcia A. , Miñambres A. , Labad J. , Pertusa A. , Bueno B. , Jiménez-Murcia S. , Menchón J. M.
Published: March 2010

Background

The same executive dysfunctions and alterations in neuroimaging tests (both functional and structural) have been found in obsessive-compulsive patients and their first-degree relatives. These neurobiological findings are considered to be intermediate markers of the disease. The aim of our study was to assess verbal and non-verbal memory in unaffected first-degree relatives, in order to determine whether these neuropsychological functions constitute a new cognitive marker for obsessive-compulsive disorder (OCD).

Method

Recall and use of organizational strategies in verbal and non-verbal memory tasks were measured in 25 obsessive-compulsive patients, 25 unaffected first-degree relatives and 25 healthy volunteers.

Results

First-degree relatives and healthy volunteers did not show differences on most measures of verbal memory. However, during the recall and processing of non-verbal information, deficits were found in first-degree relatives and patients compared with healthy volunteers.

Conclusions

The presence of the same deficits in the execution of non-verbal memory tasks in OCD patients and unaffected first-degree relatives suggests the influence of certain genetic and/or familial factors on this cognitive function in OCD and supports the hypothesis that deficits in non-verbal memory tasks could be considered as cognitive markers of the disorder.
Reducibility for a class of nonlinear quasi-periodic differential equations with degenerate equilibrium point under small perturbation
Authors: XU JUNXIANG , JIANG SHUNJUN
Published: March 2010

In this paper, using the Kolmogorov–Arnold–Moser method we prove reducibility of a class of nonlinear quasi-periodic differential equation with degenerate equilibrium point under small perturbation and obtain a quasi-periodic solution near the equilibrium point.
Phonological development of word-initial Korean obstruents in young Korean children
Authors: KIM MINJUNG , STOEL-GAMMON CAROL
Published: March 2010

This study investigates the acquisition of word-initial Korean obstruents (i.e. stops, affricates and fricatives). Korean obstruents are characterized by a three-way contrast among stops and affricates (i.e. fortis, aspirated and lenis) and a two-way fricative contrast (i.e. fortis and lenis). All these obstruents are voiceless word-initially. Cross-sectional data were collected from forty Korean children aged 2 ; 6 (year;month), 3 ; 0, 3 ; 6 and 4 ; 0, and the acquisition patterns of Korean obstruents were explored based on productions of mono- and multisyllabic words. Results confirm the universal patterns: stops were acquired before affricates and fricatives. In terms of order of acquisition across different laryngeal types, lenis stops were the last to be acquired. For Korean fricatives, in contrast, the lenis category appears to be acquired earlier than the fortis category. This study proposes that this order of acquisition may be explained by articulatory complexity associated with language-specific phonetic properties.
Volume change associated with formation and dissociation of hydrate in sediment
Authors: Lee J. Y. , Santamarina J. Carlos , Ruppel C.
Published: March 2010

Gas hydrate formation and dissociation in sediments are accompanied by changes in the bulk volume of the sediment and can lead to changes in sediment properties, loss of integrity for boreholes, and possibly regional subsidence of the ground surface over areas where methane might be produced from gas hydrate in the future. Experiments on sand, silts, and clay subject to different effective stress and containing different saturations of hydrate formed from dissolved phase tetrahydrofuran are used to systematically investigate the impact of gas hydrate formation and dissociation on bulk sediment volume. Volume changes in low specific surface sediments (i.e., having a rigid sediment skeleton like sand) are much lower than those measured in high specific surface sediments (e.g., clay). Early hydrate formation is accompanied by contraction for all soils and most stress states in part because growing gas hydrate crystals buckle skeletal force chains. Dilation can occur at high hydrate saturations. Hydrate dissociation under drained, zero lateral strain conditions is always associated with some contraction, regardless of soil type, effective stress level, or hydrate saturation. Changes in void ratio during formation‐dissociation decrease at high effective stress levels. The volumetric strain during dissociation under zero lateral strain scales with hydrate saturation and sediment compressibility. The volumetric strain during dissociation under high shear is a function of the initial volume average void ratio and the stress‐dependent critical state void ratio of the sediment. Other contributions to volume reduction upon hydrate dissociation are related to segregated hydrate in lenses and nodules. For natural gas hydrates, some conditions (e.g., gas production driven by depressurization) might contribute to additional volume reduction by increasing the effective stress.
Source materials for inception stage Hawaiian magmas: Pb‐He isotope variations for early Kilauea
Authors: Hanyu Takeshi , Kimura Jun‐Ichi , Katakuse Maiko , Calvert Andrew T. , Sisson Thomas W. , Nakai Shun'ichi
Published: March 2010

New noble gas and radiogenic isotopic compositions are presented for tholeiitic, transitional, and alkalic rocks from the submarine Hilina region on the south flank of Kilauea, Hawaii. The 3He/4He ratios for undegassed glass and olivine separates (11–26 Ra) contrast with those of postshield and rejuvenated alkalic lavas, consistent with the alkalic and transitional basalts at Hilina corresponding to early Kilauea magmas. Most early Kilauea samples contain highly radiogenic Pb isotopes compared with other Hawaiian rocks and therefore derive from a Hawaiian plume end‐member source (here referred to as the Hilina component) distinctive in that respect. Besides radiogenic Pb isotopes, the Hilina component has relatively low 3He/4He (<12 Ra) among the Hawaiian magmas. Hawaiian inception stage magmas, including Hilina, Loihi, and deep Hana Ridge (east Maui), define a linear array in 206Pb/204Pb‐3He/4He isotope space, indicating that mixing between the Hilina and Loihi components (or their melts) dominates magmatism at the leading edge of the Hawaiian plume. The Hilina component's isotopic characteristics can be derived from young subduction‐recycled crust or metasomatised mantle. The isotopic differences between the geographically discriminated Kea and Loa trend volcanic chains, observed in shield stage lavas, are also seen in the inception stage magmas, suggesting that proportions of melts derived from the Hilina and Loihi components were different between the Kea and Loa trend volcanoes.
Committee of Visitors Advises NSF Division of Ocean Sciences
Authors: Fine Rana , Beardsley Robert , Bontempi Paula , Campbell Janet , Chotiros Nick , Klein Emily , North Elizabeth , Olsen Curtis , Robles Carlos , Seyfried William , Thomas Debbie
Published: March 2010

The U.S. National Science Foundation (NSF) relies on external Committees of Visitors (COV) convened every 3 years to assess the quality and integrity of program operations and program‐level technical and managerial matters pertaining to proposal decisions. Members of COVs are chosen by program officers and division directors to represent scientific diversity, in terms of disciplines, institutions, and potential principal investigators (PIs).

One such COV recently assessed NSF's Ocean Sciences (OCE) division. The COV for OCE found that the science receiving funding is highly relevant to the overarching objectives of NSF and that the OCE peer‐review process is robust. Further, the COV found that program officers—NSF staff who manage programs in ocean sciences and administer proposals and grants—are conscientious and are funding projects of top quality that are well balanced across a broad spectrum.
2010 Election Results
Authors: Bamzai Anjuli , Robinson Robert , Shirey Steven
Published: March 2010

On 3 February 2010, AGU members completed voting for Union and section officers and for directors for the newly approved Board of Directors. Access to voting was provided over the Internet for a period of 31 days. Paper ballots were available upon request. Voting results and analysis were prepared by AGU staff, with results certified by AGU's Tellers Committee on 4 February 2010. Voting was widespread throughout the global base of AGU members. The overall participation rate was 19.2%.
Volunteers: A Critical Element in the New AGU
Authors: McPhaden Michael
Published: March 2010

We are in the midst of unprecedented change at the American Geophysical Union. Members have recently approved new bylaws to create a governance structure that better reflects the Union's diverse range of scientific interests and enables more efficient and transparent functioning of the organization. We have also embarked on a new strategic planning process to develop far‐reaching organizational goals that will ensure continued global leadership in the Earth and space sciences. Finally, we are in the midst of hiring a new permanent executive director to lead our organization in the years ahead.
Huybers, Ishii, and Weiss Receive 2009 James B. Macelwane Medals
Authors: Schrag Daniel P. , Huybers Peter J. , Mitrovica Jerry X. , Ishii Miaki , Zuber Maria T. , Weiss Benjamin P.
Published: March 2010

Peter J. Huybers, Miaki Ishii, and Benjamin P. Weiss were awarded the 2009 James B. Macelwane Medal at the AGU Fall Meeting Honors Ceremony, held on 16 December 2009 in San Francisco, Calif. The medal is for “significant contributions to the geophysical sciences by a young scientist of outstanding ability.”