bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sonographic thymic measurements in Down syndrome fetuses
Authors: De Leon‐Luis Juan , Santolaya Joaquín , Gamez Francisco , Pintado Pilar , Perez Ricardo , Ortiz‐Quintana Luis 
Published: July 2011

AbstractObjectiveChildren with Down syndrome (DS) can have hypoplastic thymuses with an impaired capacity to liberate newly generated T cells. We sought to determine if the size of the thymus in DS fetuses is different from control fetuses.MethodsWe performed comprehensive prenatal sonographic evaluation that included measurements of the thymus in 874 control fetuses and in 12 DS fetuses. We used graphic comparisons between thymic measurements obtained from the two groups of fetuses and a nested case‐control validation study in which DS fetuses were matched for gestational age with control fetuses using a 2‐to‐1 ratio to make group comparisons.ResultsThe plot analysis showed that more than two‐thirds of DS fetuses had sonographic signs of thymic hypoplasia. The nested case‐control study confirmed that the thymus of DS fetuses was statistically smaller than the thymus of control fetuses [DS transverse diameter 12.3 mm, interquartile range (IQR) 6.2 vs control 18.1 mm, IQR 4.4; p < 0.001 and, DS perimeter 30.9 mm, IQR 20.1 vs control 48.6 mm, IQR 20.4; p < 0.01].ConclusionsOur findings suggest that the majority of DS fetuses have smaller thymuses than control. Prenatal measurements of the thymus may be clinically useful in the management of DS pregnancies. Copyright © 2011 John Wiley & Sons, Ltd.
Exposure to antipsychotic medications over a 4‐year period among children who initiated antipsychotic treatment before their sixth birthday
Authors: Constantine Robert J. , Jentz Susan , Bengtson Michael , McPherson Marie , Andel Ross , Jones Mary Beth 
Published: July 2011

ABSTRACTPurposeThis study aims the following: (i) to describe the exposure to antipsychotic medications over a 4‐year period experienced by a cohort of children who initiated antipsychotic treatment before their sixth birthday; and (ii) to identify variables associated with the risk of antipsychotic exposure.MethodsChildren were identified who initiated an index episode of antipsychotic treatment before their sixth birthday in Florida's fee for service Medicaid program. With the use of claims data, the medication utilization of these children was tracked during the year before and the 4 years following the start of their index episodes (pre‐index and four post‐index periods). Generalized estimating equations were used to identify variables associated with the risk of additional days of antipsychotic exposure.ResultsFive hundred twenty‐eight children were included in the cohort. The mean total number of days of exposure was 821.9 (± 431.9), representing 56.3% of all days during the four post‐index periods. The mean days of exposure to combinations of antipsychotics and other classes of psychotherapeutic medications were 623.8 ± 447.6 days. Children with primary diagnoses of pervasive developmental disorders and affective disorders were at greater risk of additional days of exposure than children with attention deficit/hyperactivity disorder. Exposure tended to be greater among children with indicators of clinical complexity including the presence of secondary diagnoses and the use of other classes of psychotherapeutic medications in addition to antipsychotics.ConclusionsExposure to antipsychotic mediations was extensive. Although these children may have had complex and severe problems, additional research is urgently needed on the benefits and risks of long‐term antipsychotic exposure among very young children. Copyright © 2011 John Wiley & Sons, Ltd.
Rheological hybrid effect in dually filled polycarbonate melt containing liquid crystalline polymer
Authors: Mi Qinyong , Zhang Xiaocheng , He Jiasong 
Published: July 2011

AbstractPolycarbonate (PC)/liquid crystalline polymer (LCP) blends dually filled with glass fiber and nano‐SiO2 were prepared by melt blending, with the use of a commercial Vectra A130 as the source of LCP and glass fiber. In these dually filled PC/LCP melts, rheological hybrid effect occurred, confirmed by the melt viscosity of the quadruple polymer blends decreased with increasing nano‐silica loading, influenced by the minor LCP phase in the blend. The drastic viscosity reduction closely correlates with the deformation and fibrillation of LCP droplets in the system. The LCP fibrillation was controlled jointly by the thermodynamic and hydrodynamic driving forces. Finally, the dually filled PC/LCP melt had decreased viscosity lower than those of pure PC, silica‐filled PC, and PC/Vectra A130 blends, and furthermore had decreased glass fiber breakage, shown by larger average aspect ratio than that in PC/Vectra A130 blends. POLYM. ENG. SCI., 2012. © 2011 Society of Plastics Engineers
Detecting protein complexes and functional modules from protein interaction networks: A graph entropy approach
Authors: Kenley Edward Casey , Cho Young‐Rae 
Published: July 2011

AbstractRecent high‐throughput experiments have generated protein–protein interaction data on a genomic scale, yielding the complete interactome for several organisms. Various graph clustering algorithms have been applied to protein interaction networks for identifying protein complexes and functional modules. Although the previous algorithms are scalable and robust, their accuracy is still limited because of the complex connectivity found in protein interaction networks. In this study, we propose a novel information‐theoretic definition, graph entropy, as a measure of the structural complexity of a graph. Loss of graph entropy represents an increase in modularity of the graph. Based on this concept, we present a graph clustering algorithm which searches for the local optimum in modularity. The algorithm detects each optimal cluster by growing a seed in a manner that minimizes graph entropy. In the experiments with the yeast interactome, the results show that the graph entropy approach has higher accuracy in predicting protein complexes and functional modules than the best competing method. We statistically compared output clusters to both known protein complexes and Gene Ontology annotations in the biological process and molecular function categories in order to measure f‐scores and p‐scores as clustering accuracy. Because this algorithm is also scalable, it can be applied to the larger scale human protein interaction network.
A survey of hemoglobin quaternary structures
Authors: Dey Sucharita , Chakrabarti Pinak , Janin Joël 
Published: July 2011

AbstractWe perform an analysis of the quaternary structure and dimer/dimer interface in the crystal structures of 165 human hemoglobin tetramers; 112 are in the T, 17 the R, 14 the Y (or R2) state; 11 are high‐affinity T state mutants, and 11 may either be intermediates between the states, or off the allosteric transition pathway. The tertiary structure is fixed within each state, in spite of the different ligands, mutations, and chemical modifications present in individual entries. The geometry of the tetramer assembly is essentially the same in all the R or the Y state entries; it is slightly different in high salt and low salt crystals of T state hemoglobins. The dimer/dimer interface differs in terms of size, chemical composition and polar interactions, between the states. It is loosely packed, like crystal packing contacts or the subunit interface of weakly associated homodimers, and unlike most oligomeric proteins, which have close‐packed interfaces. The loose packing is most obvious in the liganded forms, where the tetramer is known to dissociate at low concentration. We identify cavities that contribute to the loose packing of the α1β2 and α2β1 contacts. Two pairs of cavities occur recurrently in both the T and the R state tetramers. They may contribute to the allosteric mechanism by facilitating the subunit movements and the tertiary structure changes that accompany the transition from T to R to Y. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Antibody modeling assessment
Authors: Almagro Juan C. , Beavers Mary Pat , Hernandez‐Guzman Francisco , Maier Johannes , Shaulsky Jodi , Butenhof Kenneth , Labute Paul , Thorsteinson Nels , Kelly Kenneth , Teplyakov Alexey , Luo Jinquan , Sweet Raymond , Gilliland Gary L. 
Published: July 2011

AbstractA blinded study to assess the state of the art in three‐dimensional structure modeling of the variable region (Fv) of antibodies was conducted. Nine unpublished high‐resolution x‐ray Fab crystal structures covering a wide range of antigen‐binding site conformations were used as benchmark to compare Fv models generated by four structure prediction methodologies. The methodologies included two homology modeling strategies independently developed by CCG (Chemical Computer Group) and Accerlys Inc, and two fully automated antibody modeling servers: PIGS (Prediction of ImmunoGlobulin Structure), based on the canonical structure model, and Rosetta Antibody Modeling, based on homology modeling and Rosetta structure prediction methodology. The benchmark structure sequences were submitted to Accelrys and CCG and a set of models for each of the nine antibody structures were generated. PIGS and Rosetta models were obtained using the default parameters of the servers. In most cases, we found good agreement between the models and x‐ray structures. The average rmsd (root mean square deviation) values calculated over the backbone atoms between the models and structures were fairly consistent, around 1.2 Å. Average rmsd values of the framework and hypervariable loops with canonical structures (L1, L2, L3, H1, and H2) were close to 1.0 Å. H3 prediction yielded rmsd values around 3.0 Å for most of the models. Quality assessment of the models and the relative strengths and weaknesses of the methods are discussed. We hope this initiative will serve as a model of scientific partnership and look forward to future antibody modeling assessments. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Assessment of protein structure refinement in CASP9
Authors: MacCallum Justin L. , Pérez Alberto , Schnieders Michael J. , Hua Lan , Jacobson Matthew P. , Dill Ken A. 
Published: July 2011

AbstractWe assess performance in the structure refinement category in CASP9. Two years after CASP8, the performance of the best groups has not improved. There are few groups that improve any of our assessment scores with statistical significance. Some predictors, however, are able to consistently improve the physicality of the models. Although we cannot identify any clear bottleneck in improving refinement, several points arise: (1) The refinement portion of CASP has too few targets to make many statistically meaningful conclusions. (2) Predictors are usually very conservative, limiting the possibility of large improvements in models. (3) No group is actually able to correctly rank their five submissions—indicating that potentially better models may be discarded. (4) Different sampling strategies work better for different refinement problems; there is no single strategy that works on all targets. In general, conservative strategies do better, while the greatest improvements come from more adventurous sampling—at the cost of consistency. Comparison with experimental data reveals aspects not captured by comparison to a single structure. In particular, we show that improvement in backbone geometry does not always mean better agreement with experimental data. Finally, we demonstrate that even given the current challenges facing refinement, the refined models are useful for solving the crystallographic phase problem through molecular replacement. Proteins 2011;. © 2011 Wiley‐Liss, Inc.
Sampling‐based exploration of folded state of a protein under kinematic and geometric constraints
Authors: Yao Peggy , Zhang Liangjun , Latombe Jean‐Claude 
Published: July 2011

AbstractFlexibility is critical for a folded protein to bind to other molecules (ligands) and achieve its functions. The conformational selection theory suggests that a folded protein deforms continuously and its ligand selects the most favorable conformations to bind to. Therefore, one of the best options to study protein‐ligand binding is to sample conformations broadly distributed over the protein‐folded state. This article presents a new sampler, called kino‐geometric sampler (KGS). This sampler encodes dominant energy terms implicitly by simple kinematic and geometric constraints. Two key technical contributions of KGS are (1) a robotics‐inspired Jacobian‐based method to simultaneously deform a large number of interdependent kinematic cycles without any significant break‐up of the closure constraints, and (2) a diffusive strategy to generate conformation distributions that diffuse quickly throughout the protein folded state. Experiments on four very different test proteins demonstrate that KGS can efficiently compute distributions containing conformations close to target (e.g., functional) conformations. These targets are not given to KGS, hence are not used to bias the sampling process. In particular, for a lysine‐binding protein, KGS was able to sample conformations in both the intermediate and functional states without the ligand, while previous work using molecular dynamics simulation had required the ligand to be taken into account in the potential function. Overall, KGS demonstrates that kino‐geometric constraints characterize the folded subset of a protein conformation space and that this subset is small enough to be approximated by a relatively small distribution of conformations. Proteins 2012. © 2011 Wiley Periodicals, Inc.
Guinean coastal rainfall of the West African Monsoon
Authors: Nguyen Hanh , Thorncroft Chris D. , Zhang Chidong 
Published: July 2011

AbstractThe nature and variability of the springtime rainfall onset at the Guinean coast is explored. The coastal onset is defined as the time when the oceanic extent of the rain band crosses the Equator. The oceanic extent is defined as the location where the rain rate falls below 2 mm day−1. The mean coastal onset averaged over 1979–2009 from Global Precipitation Climatology Project (GPCP) rainfall data is on 11 May with a standard deviation of 14.5 days. This result is robust and seen in different rainfall products. The coastal rainfall demise is determined as the time when simultaneously the peak rainfall at the coast weakens and the rainfall over the Sahel intensifies. The mean coastal demise is 26 June with a standard deviation of 9.5 days. This implies that the mean length of the coastal phase is 47 days with a standard deviation of 13 days. The coastal onset and its demise are primarily driven by changes in sea‐surface temperature (SST) between the Guinean coast and the Equator. There exists a 301 K threshold below which the equatorial cold tongue develops rapidly and leads to the coastal onset 10 days later. The same threshold applies to SSTs near the coast, where the water cooling precedes the end of the coastal rain phase by 16 days. Sea‐surface temperature anomalies in the southeast Atlantic in winter are potentially a predictor for the coastal rainfall variability in spring. Copyright © 2011 Royal Meteorological Society
Comparison of Pearson distribution system and response modeling methodology (RMM) as models for process capability analysis of skewed data
Authors: Shauly Michal , Parmet Yisrael 
Published: July 2011

AbstractClements' approach to process capability analysis for skewed distributions, based on fitting the Pearson distribution system to data, is widely used in industry. In this paper we compare the accuracy of the Pearson system and the RMM (response modeling methodology) distribution, as distributional models for process capability analysis of non‐normal data. The accuracy of the estimates of Cp and CPU is measured by the relative mean square errors. Three factors that may affect the accuracy of RMM and Pearson are examined: the data‐generating distribution (Weibull, log‐normal, gamma), the skewness (0.5, 1.25, 2) and the sample size (50, 300, 2000). The results show that RMM consistently outperforms Pearson, even for samples from gamma, which is a special case of Pearson. This implies that when observations are visibly skewed yet their underlying distribution is unknown, RMM estimators for Cp and CPU take account of the information stored in the data more precisely than the Pearson model, and may therefore constitute a preferred distributional model to pursue in process capability analysis. Copyright © 2011 John Wiley & Sons, Ltd.
SERVQUAL and the process improvement challenge
Authors: McCollin Chris , Ograjenšek Irena , Göb Rainer , Ahlemeyer‐Stubbe Andrea 
Published: July 2011

AbstractService quality is difficult to quantify as it is a function of differing customer perceptions over time, the ever changing market conditions, the measurement process and the interpretation of the data that have been gathered. The SERVQUAL questionnaire and gap analysis have been used to analyse service quality within diverse organisations over the last 30 years. The measurement instrument has been analysed, changed and criticized by numerous authors. However, as a stand‐alone tool, it has remained much the same. With organisational emphasis on change in systems as well as new and innovative ways of using computer technology, SERVQUAL is more likely to become obsolete as a stand‐alone tool as new ways of collecting and disseminating data become available. However, it might survive if integrated into an ever changing IT framework within a generic company structure such as e.g. the Six Sigma framework. In our paper we strive (1) to find out to what extent is SERVQUAL helpful in process improvement; and (2) to determine characteristics of methodology that would call for application of SERVQUAL for process improvement purposes. Copyright © 2011 John Wiley & Sons, Ltd.
Measurement uncertainty with nested mixed effect models
Authors: Deldossi L. , Zappa D. 
Published: July 2011

AbstractMeasurement uncertainty in experiments is receiving increasing interest among practitioners both for quantitative and qualitative evaluations. Applications may be found, for example, to compare experiments run in different laboratories, to certify the precision of gauges used in the masurement process or to measure uncertainty in a classification process, i.e. when objects are qualitatively evaluated by appraisers. In this paper, after having briefly presented how to measure uncertainty using gauge repeatability and reproducibility studies, we focus on a problem quite relevant for practitioners: how to deal with the presence of correlation among ‘replications’. This issue is common to many food/agriculture experiments. By a modification of a nested mixed effect design, we describe the impact of dependencies among replications on measurement capability. Copyright © 2011 John Wiley & Sons, Ltd.
FoxO3a Functions as a Key Integrator of Cellular Signals That Control Glioblastoma Stem-like Cell Differentiation and Tumorigenicity
Authors: Sunayama Jun , Sato Atsushi , Matsuda Ken-Ichiro , Tachibana Ken , Watanabe Eriko , Seino Shizuka , Suzuki Kaori , Narita Yoshitaka , Shibui Soichiro , Sakurada Kaori , Kayama Takamasa , Tomiyama Arata , Kitanaka Chifumi 
Published: July 2011

Abstract
Glioblastoma is one of the most aggressive types of human cancer, with invariable and fatal recurrence even after multimodal intervention, for which cancer stem-like cells (CSLCs) are now being held responsible. Our recent findings indicated that combinational inhibition of phosphoinositide-3-kinase/Akt/mammalian target of rapamycin (mTOR) and mitogen-activated protein/extracellular signal-regulated kinase kinase (MEK)/extracellular signal-regulated kinase (ERK) pathways effectively promotes the commitment of glioblastoma CSLCs to differentiation and thereby suppresses their tumorigenicity. However, the mechanism by which these two signaling pathways are coordinated to regulate differentiation and tumorigenicity remains unknown. Here, we identified FoxO3a, a common phosphorylation target for Akt and ERK, as a key transcription factor that integrates the signals from these pathways. Combinational blockade of both the pathways caused nuclear accumulation and activation of FoxO3a more efficiently than blockade of either alone, and promoted differentiation of glioblastoma CSLCs in a FoxO3a expression-dependent manner. Furthermore, the expression of a constitutively active FoxO3a mutant lacking phosphorylation sites for both Akt and ERK was sufficient to induce differentiation and reduce tumorigenicity of glioblastoma CSLCs. These findings suggest that FoxO3a may play a pivotal role in the control of differentiation and tumorigenicity of glioblastoma CSLCs by the PI3K/Akt/mTOR and MEK/ERK signaling pathways, and also imply that developing methods targeting effective FoxO3a activation could be a potential approach to the treatment of glioblastoma.
Can we place tension‐free vaginal tape where it should be? The one‐third rule
Authors: Kociszewski J. , Rautenberg O. , Kuszka A. , Eberhard J. , Hilgers R. , Viereck V. 
Published: July 2011

AbstractObjectivesThe tension‐free vaginal tape (TVT) insertion technique generally does not take into account individual urethral length. In this study we investigated whether preoperative sonographic measurement of individual urethral length allows for reliable TVT positioning under the midurethra, which is a critical segment for the continence mechanism.MethodsUrethral length was measured by preoperative introital ultrasonography in 102 consecutive female patients with stress urinary incontinence. TVT procedures were performed as recommended by the manufacturer. The suburethral incisions were initiated at one‐third of the sonographically measured urethral length. TVT position and tape–urethra distance were followed up 6 months postoperatively.ResultsAt 6‐month examination of the 102 study participants, 93.1% were cured and 6.9% showed improved continence. TVTs were found in the target range of 50–70% of the urethral length in 88.2% of the cohort. Women with the TVT in the 50–70% urethral length range and a 3–5‐mm tape–longitudinal smooth muscle distance had a greater likelihood of being cured without complications (P < 0.001).ConclusionsPreoperative sonographic measurement of urethral length, combined with the one‐third rule, may aid in reliable midurethral TVT positioning. Copyright © 2012 ISUOG. Published by John Wiley & Sons, Ltd.
Coupled‐cluster theory and its equation‐of‐motion extensions
Authors: Bartlett Rodney J. 
Published: July 2011

AbstractCoupled‐cluster theory offers today's reference quantum chemical method for most of the problems encountered in electronic structure theory. It has been instrumental in establishing the now well‐known paradigm of converging, many‐body methods,

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Many‐body perturbation theory (MBPT) for second, MBPT2, and fourth‐order MBPT4; and coupled‐cluster (CC) theory for different categories of excitations, singles, doubles, triples, quadruples (SDTQ). Although built on the same basic concept as configuration interaction (CI), many‐body methods fundamentally improve upon CI approximations by introducing the property of size extensivity, meaning that contrary to any truncated CI all terms properly scale with the number of electrons in the problem. This fundamental aspect of many‐electron methods leads to the exceptional performance of CC theory and its finite‐order MBPT approximations plus its equation‐of‐motion extensions for excited, ionized, and electron attached states. This brief overview will describe formal aspects of the theory which should be understood by perspective users of CC methods. We will also comment on some current developments that are improving the theory's accuracy or applicability. © 2011 John Wiley & Sons, Ltd.This article is categorized under:

Electronic Structure Theory > Ab Initio Electronic Structure Methods