bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prognostic value of lymphangiogenesis in supraglottic laryngeal carcinoma
Authors: Lin J Y , Li X Y , Dong P , Nakashima T 
Published: July 2011

AbstractBackground:Metastasis to regional lymph nodes via lymphatic microvessels plays a key role in cancer progression, and is an important prognostic factor in many cancers. Recent evidence suggests that tumour lymphangiogenesis promotes lymphatic metastasis.Aims:To investigate whether tumour lymphatic microvessel density correlates with clinicopathological factors and serves as a prognostic indicator of supraglottic laryngeal carcinoma progression.Methods:The lymphatics of 84 supraglottic laryngeal carcinoma cases were investigated by immunohistochemical staining for podoplanin (also termed D2-40). The relationships between (intra- and peritumoural) lymphatic microvessel density, clinicopathological parameters and clinical prognosis were analysed.Results:There was a significant relationship between high intratumoural lymphatic microvessel density and aggressive tumour node stage (p < 0.0001), distant metastasis (p = 0.037) and poor prognosis (p = 0.011), and between high peritumoural lymphatic microvessel density and node stage (p = 0.004) and poor prognosis (p = 0.029). Patients with high lymphatic microvessel density also had significantly worse disease-free survival (p = 0.003) and overall survival (p = 0.005). Intratumoural lymphatic microvessel density was found to be an independent prognostic factor for overall survival (p = 0.008) and disease-free survival (p = 0.005) (multivariate analysis).Conclusion:Lymphatic microvessel density (detected by podoplanin immunohistochemistry), especially intratumoural density, may be an independent predictor of lymphatic tumour spread and survival in supraglottic laryngeal carcinoma patients, and may be useful to guide decisions regarding additional surgery.
The Boltzmann relation and its validity in magnetized plasmas
Authors: FRANKLIN R. N. 
Published: July 2011

AbstractThis paper is concerned to give a definitive account of a physical situation of current practical interest by examining the plasma solution for a plasma in coaxial geometry with an applied axial magnetic field. It builds on earlier work concerned with plasma diamagnetism and concentrates on the parameters involved at low pressures and low collisionalities but can be extended to situations where the ions are magnetized.
Instability of electromagnetic waves with radial polarization in a rotating relativistic electron beam guided by ion channel
Authors: MIRZANEJHAD SAEED , SOHBATZADEH FARSHAD , HEIDARI ZAHRA 
Published: July 2011

AbstractDispersion characteristics of electromagnetic waves with radial and azimuthal polarization in a rotating relativistic electron beam guided by an ion channel are investigated. Ion-channel electrostatic field and self-fields of relativistic electron beam were included in the formalism. It is shown that the wave with radial polarization is unstable in two regions due to coupling with fast space charge wave. The behaviors of the instability magnitude and spread are analyzed as a function of equilibrium parameters. The introduced instability can be used for amplification and production of high-intensity laser pulse with radial polarization.
Design and analysis of CICABOT: a novel translational parallel manipulator based on two 5-bar mechanisms
Authors: Ruiz-Torres M. F. , Castillo-Castaneda E. , Briones-Leon J. A. 
Published: July 2011

SUMMARYThis work presents the CICABOT, a novel 3-DOF translational parallel manipulator (TPM) with large workspace. The manipulator consists of two 5-bar mechanisms connected by two prismatic joints; the moving platform is on the union of these prismatic joints; each 5-bar mechanism has two legs. The mobility of the proposed mechanism, based on Gogu approach, is also presented. The inverse and direct kinematics are solved from geometric analysis. The manipulator's Jacobian is developed from the vector equation of the robot legs; the singularities can be easily derived from Jacobian matrix. The manipulator workspace is determined from analysis of a 5-bar mechanism; the resulting workspace is the intersection of two hollow cylinders that is much larger than other TPM with similar dimensions.
Adaptive computed torque control for a parallel manipulator with redundant actuation
Authors: Shang Wei-Wei , Cong Shuang , Ge Yuan 
Published: July 2011

SUMMARYAn adaptive computed torque (ACT) controller in the task space is proposed for the trajectory tracking of a parallel manipulator with redundant actuation. The dynamic model, including the active joint friction, is established in the task space for the parallel manipulator, and the linear parameterization expression with respect to the dynamic and friction parameters is formulated. On the basis of the dynamic model, a new control law, which contains adaptive dynamics compensation, friction compensation, and tracking error elimination terms, is designed. After defining the state-space model of the error system, the parameter adaptation law is derived by using the Lyapunov method, and the convergence of the tracking error and the error rate is proved by using the Barbalat's lemma. The ACT controller is implemented in the trajectory tracking experiments of an actual 2-DOF parallel manipulator with redundant actuation, and the experiment results are compared with the computed torque controller.
A novel three degrees of freedom partially decoupled robot with linear actuators
Authors: Gallardo-Alvarado Jaime , Alici Gürsel , Rodríguez-Castro Ramón 
Published: July 2011

SUMMARYIn this work, a new translational robot formed with two different parallel manipulators with a common control point is introduced. An asymmetric parallel manipulator provides three translational degrees of freedom to the proposed robot while the orientation of the end-effector platform is kept constant by means of a Delta-like manipulator. An exact solution is easily derived to solve the forward displacement analysis while a semi-closed form solution is available for solving the inverse displacement analysis. The infinitesimal kinematics of the robot is approached by applying the theory of screws. Finally, a numerical example that consists of solving the inverse/forward displacement analysis as well as the forward acceleration analysis of the end-effector platform is presented. The example also includes the computation of the workspace and the direct/inverse singularities of the example.
Toddlers learn words in a foreign language: the role of native vocabulary knowledge
Authors: KOENIG MELISSA , WOODWARD AMANDA L. 
Published: July 2011

ABSTRACTThe current study examined monolingual English-speaking toddlers' (N=50) ability to learn word–referent links from native speakers of Dutch versus English, and second, whether children generalized or sequestered their extensions when terms were tested by a subsequent speaker of English. Overall, children performed better in the English than in the Dutch condition; however, children with high native vocabularies successfully selected the target object for terms trained in fluent Dutch. Furthermore, children with higher vocabularies did not indicate their comprehension of Dutch terms when subsequently tested by an English speaker whereas children with low vocabulary scores responded at chance levels to both the original Dutch speaker and the second English speaker. These findings demonstrate that monolingual toddlers with proficiency in their native language are capable of learning words outside of their conventional system and may be sensitive to the boundaries that exist between language systems.
Trajectories of faithfulness in child-specific phonology
Authors: Becker Michael , Tessier Anne-Michelle 
Published: July 2011

AbstractThis paper provides new evidence and analysis of gradual and U-shaped phonological learning. Using a rich longitudinal corpus from Trevor (Compton & Streeter 1977, Pater 1997b) we demonstrate that some of Trevor's consonant harmony follows a statistically significant U-shaped trajectory, in contrast to the more typical S-shaped progression of his complex onsets. We then analyse these two developmental paths using an OT model of phonological acquisition (Hayes 2004, Prince & Tesar 2004, Tessier 2007, 2009), in which the learner's variation within and across stages is the effect of stored old productions rather than a variable grammar. The decrease in Trevor's faithfulness to place of articulation due to consonant harmony is attributed to the induction of a new constraint during the course of learning. Our analysis is paired with a computational implementation, showing how competition between old forms and the current grammar allows the model to derive both S-shaped and U-shaped patterns.
Explaining sonority projection effects
Authors: Daland Robert , Hayes Bruce , White James , Garellek Marc , Davis Andrea , Norrmann Ingrid 
Published: July 2011

AbstractThe termsonority projectionrefers to behavioural distinctions speakers make between unattested phonological sequences on the basis of sonority. For example, among onset clusters, the well-formedness relation [bn]>[lb] is observed in speech perception, speech production and non-word acceptability (Davidson 2006, 2007, Berentet al.2007, Albright, ms). We begin by replicating the sonority projection effects in a non-word acceptability study. Then we evaluate the extent to which sonority projection is predicted by existing computational models of phonotactics (Coleman & Pierrehumbert 1997, Hayes & Wilson 2008,inter alia). We show that a model based only on lexical statistics can explain sonority projection in English without a pre-existing sonority sequencing principle. To do this, a model must possess (i) a featural system supporting sonority-based generalisations, and (ii) a context representation including syllabification or equivalent information.
Migratory bird species in young tropical forest restoration sites: effects of vegetation height, planting design, and season
Authors: LINDELL CATHERINE A. , COLE REBECCA J. , HOLL KAREN D. , ZAHAWI RAKAN A. 
Published: July 2011

SummaryTropical land cover change has negatively affected numerous migratory bird populations. Forest restoration can augment migrant wintering habitat. However, almost no information exists about factors that influence migrant use of tropical restoration sites. We sampled migrant birds in young restoration sites in Costa Rica from February 2006 to April 2008 to determine how vegetation height, planting design, season, and landscape forest cover influenced capture rates of four declining species. We also documented total numbers of migratory species and individuals captured in each planting design treatment; each site had a control treatment where seedlings were not planted, an island treatment where seedlings were planted in patches, and a plantation treatment where seedlings were planted to cover the entire area. Sites varied in landscape forest cover within 500 m buffers. Three out of four focal species were captured significantly more often in plantation treatments than island or control treatments. Two of the four species showed seasonal patterns and one species was captured more often in high-vegetation sites. Greater numbers of species and individuals were captured in plantation treatments compared to island and control treatments. The plantation planting design increased migrant use more quickly than the island planting design. When resources are available, we recommend planting plantation-style to rapidly increase the value of restoration sites to a range of species, particularly those that use woody vegetation. When resources are more limited, planting islands may be a cost-effective, although not as ecologically effective, alternative that supports a diversity of migrant species compared to unplanted controls.
Serum and pulmonary vascular endothelial growth factor/receptors and haemodynamic measurements in cyanotic congenital heart disease with decreased pulmonary blood flow
Authors: Tolunay İlknur , Tunaoglu Sedef , Akyürek Nalan , Halid Velit , Olgunturk Rana , Kula Serdar 
Published: July 2011

AbstractTetralogy of Fallot is the most common cyanotic congenital heart disease with decreased pulmonary blood flow. Right-to-left shunt and infundibular pulmonary stenosis in this disease lead to a decrease in arterial O2 saturation. Hypoxia is a strong stimulus for angiogenesis; however, the reason for insufficiency in the pulmonary vascular growth in patients despite chronic arterial hypoxia is still not known. This study was planned considering that the impairment in vascular endothelial growth factor-receptor relationship or the vascular endothelial growth factor-receptor deficiency in the pulmonary vascular bed during development may cause insufficiency of pulmonary vascular growth. A total of 24 patients were grouped as cyanotic – including 13 patients with tetralogy of Fallot – and acyanotic – including 11 patients with left-to-right shunt lesions. During cardiac catheterisation, vascular endothelial growth factor measurements were performed; and oxygen saturations, pressures, and haemoglobin levels were measured. Perioperative lung biopsy for vascular endothelial growth factor receptors was performed in the cyanotic group. Vascular endothelial growth factor of the aorta was higher in the acyanotic group. There was a significant negative correlation between vascular endothelial growth factor levels and aortic O2 saturation in the cyanotic group (p < 0.05). Vascular endothelial growth factor tissue staining was negative in 11 out of 13 (84.6%) patients. KDR/Flk-1 receptor was positive in four out of 13 (30.7%) patients; Flt-1 receptor was positive in six out of 13 (46.1%) patients. Vascular endothelial growth factor values were found to be lower than those of the acyanotic patients in this study. Low serum vascular endothelial growth factor levels of the cyanotic group, in spite of the hypoxia, demonstrated the importance of studying vascular endothelial growth factor tissue levels and vascular endothelial growth factor receptors in these patients.
d-Transposition of the great arteries in a 12-year-old child: is arterial switch still an option?
Authors: Mahima Jayaranganath , Shivanna Devananda Nijagal , Subramanian Anand 
Published: July 2011

AbstractArterial switch surgery for d-transposition of great arteries is usually performed in the first 2 weeks of life before the left ventricle regresses. The arterial switch surgery that helps achieve anatomic and physiologic correction of this condition has better long-term outcomes than other surgical approaches. The procedure may still be attempted at an older age where the left ventricle has not regressed. We report a rare case of a 12-year-old child with d-transposition of great arteries, a remote muscular ventricular septal defect and isolated valvar pulmonic stenosis, which was corrected by an arterial switch surgery.
Determination of Mineralogical Contents of a Bangle Shard from an Indus Valley Settlement through X-ray Diffraction Analysis
Authors: Kayani Saheeb Ahmed , Siddiqui Rehan ul Haq 
Published: July 2011

AbstractSome initial results of XRD testing of a bangle shard collected from Harrappa, an Indus Valley settlement located in Pakistan, are presented. The mineralogical structure of the bangle shard includes montmorillonite, gypsum, and quartz.
Molecular simulations to study the effect of pore geometry and structure on the adsorption of CH4/H2 mixtures in carbon pores
Authors: Kumar Vasanth , Müller Erich , Rodriguez-Reinoso Francisco 
Published: July 2011

AbstractWe used molecular simulations to study the effect of pore structure and geometry on the selectivity of carbon materials for the adsorption of methane from a mixture of methane and hydrogen at 50 bar and 298 K. We modeled hydrogen as a more realistic dumb-bell shaped fluid and methane as spherical Lennard-Jones sphere. The pore geometry studied includes the slit, nanotube, random carbon structure and carbon pores that mimic a foam structure. Our results confirm that both the pore size and pore structure have a significant effect on the selectivity for methane molecules. An array of nanotubes that have a closed structure has the highest selectivity for methane molecules, followed by carbon foam, slit and random pore structures. Energetic and packing effects at low and high pressures, respectively, influence the selectivity for methane. Reduction in entropy of hydrogen in smaller pores increases the selectivity for methane molecules.
Simple high-throughput annotation pipeline (SHAP)
Authors: DeMaere Matthew Z. , Lauro Federico M. , Thomas Torsten , Yau Sheree , Cavicchioli Ricardo 
Published: July 2011

Abstract
Summary: SHAP (simple high-throughput annotation pipeline) is a lightweight and scalable sequence annotation pipeline capable of supporting research efforts that generate or utilize large volumes of DNA sequence data. The software provides Grid capable analysis, relational storage and Web-based full-text searching of annotation results. Implemented in Java, SHAP recognizes the limited resources of many smaller research groups.
Availability: Source code is freely available under GPLv3 at https://sourceforge.net/projects/shap.
Contact: matt.demaere@unsw.edu.au; r.cavicchioli@unsw.edu.au
CalcTav—integration of a spreadsheet and Taverna workbench
Authors: Sroka Jacek , Krupa Łukasz , Kierzek Andrzej M. , Tyszkiewicz Jerzy 
Published: July 2011

Abstract
Motivation: Taverna workbench is an environment for construction, visualization and execution of bioinformatic workflows that integrates specialized tools available on the Internet. It already supports major bioinformatics services and is constantly gaining popularity. However, its user interface requires considerable effort to learn, and sometimes requires programming or scripting experience from its users. We have integrated Taverna with OpenOffice Calc, making the functions of the scientific workflow system available in the spreadsheet. In CalcTav, one can define workflows using the spreadsheet interface and analyze the results using the spreadsheet toolset.
Results: Technically, CalcTav is a plugin for OpenOffice Calc, which provides the functionality of Taverna available in the form of spreadsheet functions. Even basic familiarity with spreadsheets already suffices to define and use spreadsheet workflows with Taverna services. The data processed by the Taverna components is automatically transferred to and from spreadsheet cells, so all the visualization and data analysis tools of OpenOffice Calc are available to the workflow creator within one, consistent user interface.
Availability: CalcTav is available under GPLv2 from http://code.google.com/p/calctav/
Contact: sroka@mimuw.edu.pl
Identification of novel phosphorylation modification sites in human proteins that originated after the human–chimpanzee divergence
Authors: Kim Dong Seon , Hahn Yoonsoo 
Published: July 2011

Abstract
Motivation: Phosphorylation modifications of specific protein residues are involved in a wide range of biological processes such as modulation of intracellular signal networks. Here, we present the development and application of a bioinformatics procedure for systematic identification of human-specific phosphorylation sites in proteins that may have occurred after the human–chimpanzee divergence.
Results: We collected annotated human phosphorylation sites and compared each site to orthologous mammalian proteins across taxa including chimpanzee, orangutan, rhesus macaque, marmoset, mouse, dog, cow, elephant, opossum and platypus. We identified 37 human-specific gains of annotated phosphorylation sites in 35 proteins: 22 serines, 12 threonines and 3 tyrosines. The novel phosphorylation sites are situated in highly conserved segments of the protein. Proteins with novel phosphorylation sites are involved in crucial biological processes such as cell division (AURKB, CASC5, MKI67 and PDCD4) and chromatin remodeling (HIRA, HIRIP3, HIST1H1T, NAP1L4 and LRWD1). Modified phosphorylatable residues produce novel target sites for protein kinases such as cyclin-dependent kinases and casein kinases, possibly resulting in rewiring and fine-tuning of phosphorylation regulatory networks. The potential human-specific phosphorylation sites identified in this study are useful as candidates for functional analysis to identify novel phenotypes in humans.
Contact: hahny@cau.ac.kr
Supplementary information: Supplementary data are available at Bioinformatics online.
Phylogenetic relationships among superfamilies of Hymenoptera
Authors: Sharkey Michael J. , Carpenter James M. , Vilhelmsen Lars , Heraty John , Liljeblad Johan , Dowling Ashley P.G. , Schulmeister Susanne , Murray Debra , Deans Andrew R. , Ronquist Fredrik , Krogmann Lars , Wheeler Ward C. 
Published: July 2011

AbstractThe first comprehensive analysis of higher‐level phylogeny of the order Hymenoptera is presented. The analysis includes representatives of all extant superfamilies, scored for 392 morphological characters, and sequence data for four loci (18S, 28S, COI and EF‐1α). Including three outgroup taxa, 111 terminals were analyzed. Relationships within symphytans (sawflies) and Apocrita are mostly resolved. Well supported relationships include: Xyeloidea is monophyletic, Cephoidea is the sister group of Siricoidea + [Xiphydrioidea + (Orussoidea + Apocrita)]; Anaxyelidae is included in the Siricoidea, and together they are the sister group of Xiphydrioidea + (Orussoidea + Apocrita); Orussoidea is the sister group of Apocrita, Apocrita is monophyletic; Evanioidea is monophyletic; Aculeata is the sister group of Evanioidea; Proctotrupomorpha is monophyletic; Ichneumonoidea is the sister group of Proctotrupomorpha; Platygastroidea is sister group to Cynipoidea, and together they are sister group to the remaining Proctotrupomorpha; Proctotrupoidea s. str. is monophyletic; Mymarommatoidea is the sister group of Chalcidoidea; Mymarommatoidea + Chalcidoidea + Diaprioidea is monophyletic. Weakly supported relationships include: Stephanoidea is the sister group of the remaining Apocrita; Diaprioidea is monophyletic; Ceraphronoidea is the sister group of Megalyroidea, which together form the sister group of [Trigonaloidea (Aculeata + Evanioidea)]. Aside from paraphyly of Vespoidea within Aculeata, all currently recognized superfamilies are supported as monophyletic. The diapriid subfamily Ismarinae is raised to family status, Ismaridae stat. nov.© The Will Henning Society 2011.