bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractHuman 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

AbstractReliable 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

AbstractPolyglutamine 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

AbstractEnsemble 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

AbstractTransition 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

AbstractA 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

AbstractWe 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

AbstractIn 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

AbstractObjectiveTo 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.MethodsThe 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.ResultsThe 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.ConclusionThis 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

AbstractIn 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

AbstractA 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

AbstractAdvances 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

AbstractAn 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

AbstractDifferences 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.
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

AbstractFossil 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.